1999 Mustang GT with 2001 motor swap, wont fire. Please help - Ford Mustang Forum
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post #1 of 30 (permalink) Old 07-27-2011 Thread Starter
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1999 Mustang GT with 2001 motor swap, wont fire. Please help

First off thank you for taking the time to read this, I hope that you will be able to help me out in some way to get a 4 month project off the ground and back onto the streets.
I'm not a master mechanic but know just a little bit, enough to do your typical maintenance, overhauls, and swaps.
I come from a drifting background so all I've had to this point were japanese cars and I came upon this car when my uncle gave it to me. He was going to sell it to his mechanic for dirt cheap like $1000 but I wanted to experience it so he gave it to me.
Blown spark plug hole? No problem, nothing taking the head to a machine shop or a motor swap won't fix right? Wrong.....so here's my problem.


The Problem and background story on it
First off my Mustang is a 1999 (2000 model)
My uncle had an issue with the a sparkplug being blown out, got it heli coiled 2 times and after I got it done myself for a 3rd time I decided to just get another motor instead of fixing the original.

Picked up another 4.6 on Craigslist but its a "01" or "02" model
(I forget) but man what a pain this has been.
The seller claimed the motor was good, it was pulled running, so I took the guys word and went with the install.
First the motor was seized, took 1 big bottle of marvel mystery oil and 3 days to get that thing unstuck, then it turns out it was seized because it had a blown headgasket. This was after I got it unseized, slapped everything back on and tried to start it.

So now thanks to Summit Racing, it has:
new head gaskets(done properly)
new head bolts(torqued through the proper process and spec)
timing done correctly(so I hope, I don't think there's any way you can really go wrong with it since I had the book on me)

and yeah I slap everything back on, everything is grounded, wired, plugged in, fresh battery, I go to start it and it sounded like it fired a bit and was about to start but after that it just kept churning with no explosion sounds coming from the cylinders.

Now the car has been sitting there for about 7 months with 3/4 of gas in the tank. I tried putting octane booster in there but I'm sure that gas is just too bad and needs to be thrown out.

Tried to use starter fluid with 50% ether and after spraying some in the throttle body well it sounded like it wanted to start but still nothing.

I plugged in the obd2 code reader thingy and it gives me 0 error codes. I made sure everything is all hooked up and wired correctly, grounded, full battery.

So now I'm trying to rule out that it's just bad gas.

To recap in total:
1999 car 4.6 was swapped with another "01" or "02" 4.6(block only)
with everything done correctly and no full start up of the car but just a few teases.

Now for the questions

Is there any easy way to empty out the gas without dropping the tank? My tank is the Anti-siphon tank.

What if I switch out the old gas and it still doesn't fire?
(I was thinking even with the starter fluid it would get a few rotations out of it before quitting but the car didn't even fully start)

I have a theft light that blinks, could it be the factory anti theft system not allowing me to start it?
(The only other person I know who has some knowledge about mustangs told me that it could be the anti theft system, or PATS.)

I appreciate any sort of help you can give me, I'm hoping that it is just the bad gas that's not letting it fire because I did get a flame scare because I didn't hold the intake tube closed tight, so I know that it has spark.
Just hoping that my friend wasn't right about the whole anti theft, key reflash thing because that's just stupid.

Thank you for your help, I await for your reply.

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post #2 of 30 (permalink) Old 07-27-2011
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There is a way to drain the gas. It involves using a battery charger to force the fuel pump to run. Split the round connector in the rear center of the gas tank and inject 12 volts towards the fuel pump on the RD/BK and BN/PK wires.

Put a small piece of line on the fuel filter to help direct the gas into a container. If nothing comes out, reverse the leads.

Are you aware that it is highly unlikely the motor will start with any of the intake tubes disconnected? Once the starting fluid is sprayed inside it's necessary to reattach all of the intake tubes. Why? Any large amount of unmetered air will keep it from starting.

We can help rule out the reason for the no start.

Confirm that all fuses are good.

Turn the key on but do not crank. Does the theft light go out after a 3 second prove out? If not STOP and find out why.

Turn the key on and LISTEN for the fuel pump to run. If the fuel pump does not run for 3 seconds, STOP and find out why.

Cycle the key on/pause/off several times without cranking. After the 1st restart, this could help re-prime the fuel system.

Hold the throttle half way open during cranking. Does this improve starting?

Disconnect the MAF. Does this improve starting?

Perform the tests in order and post the results. Will go from there.

Remember, there are actually few no-start sensors. The CKP sensor is the most important. However, if the CKP sensor is bad or not sending a signal, there won't be any spark or fuel.

A "noid" style tester on the fuel injectors and COP's is the best way to confirm a firing pulse.

Sooooo. For the 99-04 MY, if you are seeing a COP and fuel injector pulse, this is NOT a PATS problem.

Confirm that the motor mount grounding strap to the frame rail was re-attached.


2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.
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post #3 of 30 (permalink) Old 07-27-2011 Thread Starter
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Are you aware that it is highly unlikely the motor will start with any of the intake tubes disconnected?
all tubes were closed and plugged in, its just the main tube to the throttle body I did not tighten down but had a friend hold his hand there.


Confirm that all fuses are good.
all fuses are good

Turn the key on but do not crank. Does the theft light go out after a 3 second prove out? If not STOP and find out why.
theft light blinks no matter what, and when you try to start it, the theft light actually remains on, while trying to start.

Turn the key on and LISTEN for the fuel pump to run. If the fuel pump does not run for 3 seconds, STOP and find out why.
the fuel pump is properly working and primes each time the key goes to the on position.

Cycle the key on/pause/off several times without cranking. After the 1st restart, this could help re-prime the fuel system.
tried it, didn't work

Hold the throttle half way open during cranking. Does this improve starting?
tried many variations of throttling while turning the key over nothing.

Disconnect the MAF. Does this improve starting?
Haven't tried this but will do it this weekend

Perform the tests in order and post the results. Will go from there.

Remember, there are actually few no-start sensors. The CKP sensor is the most important. However, if the CKP sensor is bad or not sending a signal, there won't be any spark or fuel.

A "noid" style tester on the fuel injectors and COP's is the best way to confirm a firing pulse.

Sooooo. For the 99-04 MY, if you are seeing a COP and fuel injector pulse, this is NOT a PATS problem.

Confirm that the motor mount grounding strap to the frame rail was re-attached.
That one is for sure attached


Thank you, I hope this car gets started this weekend.
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post #4 of 30 (permalink) Old 07-27-2011
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The check list said to "STOP and find out why". The reason is anti-theft (PATS) is preventing your car from starting. No further tests were necessary.

Until the theft light goes out, this car will NEVER start. Note, PATS can be disabled with a hand held tuner.

Have you swapped PCM or cluster? Are you positive the PCM is alive? Did you have any issues with the swap? Anything disconnected under the dash?

Are you POSITIVE that fuses F2.21, F2.34, F2.5, and F2.37 are good? Don't cut corners here. A blown fuse could easily cause this and you could be in for a world of electrical trouble shooting "hurt" for something simple.

Check out the following thread for information on how to access the cluster diagnostic. The cluster DTC's may provide clues about what's wrong.

https://www.allfordmustangs.com/forum...stic-mode.html

2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.
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post #5 of 30 (permalink) Old 07-28-2011 Thread Starter
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The check list said to "STOP and find out why". The reason is anti-theft (PATS) is preventing your car from starting. No further tests were necessary.

Until the theft light goes out, this car will NEVER start. Note, PATS can be disabled with a hand held tuner.What kind of hand held tuner? I might be taking this to a mechanic a few miles away because he's very experienced with Fords and has worked on many Mustangs so I'm sure he has it and will be able to fix it.

Have you swapped PCM or cluster? Are you positive the PCM is alive? Did you have any issues with the swap? Anything disconnected under the dash?
What's a PCM? Did not change the cluster since the motor was only 1 year newer(the motor was an original swap, I've seen some guys swap in the 5.0 into their V6, and other stuff but this is just a stock original motor replacement swap,block only. If I still needed to change the cluster then that would just boggle my mind.)
No issues with the swap except for the motor being seized and with a blown headgasket, nothing is disconnected under the dash.


Are you POSITIVE that fuses F2.21, F2.34, F2.5, and F2.37 are good? Don't cut corners here. A blown fuse could easily cause this and you could be in for a world of electrical trouble shooting "hurt" for something simple.
Yep, it was the second thing I did after checking to make sure I didn't miss any unplugged wires or grounds.

Check out the following thread for information on how to access the cluster diagnostic. The cluster DTC's may provide clues about what's wrong.
Thank you for this, I will be checking it out this weekend when I get back. That is actually really cool, I've never seen any car that does that. Except for the G35s which all they do is blink a light so many times to look up the code and tell you what's wrong.
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post #6 of 30 (permalink) Old 07-28-2011
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PCM/ECM: the car's brain.

Are you positive the round grounding connectors in the engine bay were re-connected after the swap? There are two large black wires with a white stripe. One is under the intake tube and hard to see unless you are looking for it. The other is under the battery junction box passing around the battery.

Consider measuring the key off resistance from the PCM pin #25 (Black) wire back to battery negative. Should be low. Post. Also test the BK/WH wires on pin # 3,51,77,103.

If the PCM's ground is bad, it will act as if there is no power. This WILL create a PATS fault.

You are using the correct key right? Remember there's a chip inside the key that the PATS reads on every start up. Do you have an extra key to try?

Also try locking and unlocking the driver's door and locking/unlocking the door with the remote FOB. Sometimes this will reset PATS after a battery disconnect.

Are you aware that almost any locksmith can reprogram a PATS key? This avoids having to tow to a dealer/mechanic.

Any hand held turner that is able to modify the car's tune can disable PATS.

Last edited by wmburns; 09-22-2016 at 10:09 AM.
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post #7 of 30 (permalink) Old 07-28-2011 Thread Starter
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yeah I had 2 different keys, one of the alarm remotes needs a new battery but I have one that works and did try a few combinations to see if it would shut off, but nothing happened.

I'm going to go through everything, check the ground, wiring, reconnect the battery because I take off the connectors every time I'm done working with it and try to do the remote thing.

I'm sure it's something stupid simple but for some reason it's just giving me more trouble than I need it to be.
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post #8 of 30 (permalink) Old 07-29-2011
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It would sure be helpful to my understanding if there was confirmation that the PCM is alive and talking. This could save time by not chasing "wild geese".

With the key on, do not crank. Attach an ODB2 reader or scanner and attempt to access the DTC codes.

IF the PCM does not talk to the ODB2 reader, this confirms you are dealing with a PCM problem (not PATS per se). After a motor swap, the most likely cause for a apparently dead PCM is a blown fuse or missing connector.

2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.
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post #9 of 30 (permalink) Old 07-29-2011
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if your theft light is blinking and the odometer is dashed------ out then its a PATS system. You can bypass it with a handheld programmer like SCT, diablotech, etc. Or reprogram the keys..
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post #10 of 30 (permalink) Old 07-29-2011 Thread Starter
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Quote:
Originally Posted by tobe1424 View Post
if your theft light is blinking and the odometer is dashed------ out then its a PATS system. You can bypass it with a handheld programmer like SCT, diablotech, etc. Or reprogram the keys..
Dashed------- while starting? I didn't notice anything like that, but it reads the odometer mileage for sure.

I'll be sure to check for those blown fuses again, I one time had a buddy who's car wouldn't start, and it turns out the fuse did blow, but the blow was soooooooooooo thin that it looked like they were still connected.

Tomorrow morning I will be jumping back on it, I will also take a video too so that you may see what's going on and try to trouble shoot it from there.
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post #11 of 30 (permalink) Old 07-29-2011 Thread Starter
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I just googled the whole pats issue, and on another forum some guys went through the same thing, one guy did a motor swap, another guy switched heads, and it was a 10amp fuse 3rd from the top.
Looking at one of the images I found for the fuse box relay it could be Ign SW, Fuel pump, or CN illum. Frankly it could be the first 2, so just to eliminate that possibility I'm going to replace all of the fuses or primarily the ones having an effect with the car starting.

Also when we did plug in the obd2, it came with 0 codes or 0 errors.

I'm a little bit more optimistic about the car starting this weekend, but I always have the opposite result, so I'll just keep thinking that this car is not going to start.
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1999-2004 BJB CJB fuse panel layout

The cluster mileage reading will either be all dash or a mileage. Since the cluster displays mileage and the ODB2 scanner is talking to the PCM, this confirms the PCM is working at some level.

This also adds to the theory the problem is a pure PATS issue. What bothers me is how a car that worked before the motor swap now has a PATS problem. What has changed?

As has been mentioned before, a blown F2.34, F2.21, F2.5 F2.37 fuse could "create" a PATS failure.

There are other fuses in the battery juncion box that "feed" the CJB. So a blown upstream fuse can be the root cause.

The OP states that the fuses are good. However, I have personal experience when troubleshooting a problem. 1st item was to "check" the fuse. We were wrong and thought it was good when in fact it was bad. What followed was 24 hours of wire harness trouble shooting that I will not soon forget. All of it preventable.

I will never just LOOK at a fuse ever again.

Knowing what I know now, I would pull fuse F2.34 and verify there is +12 volts with the key on to the supply side of the fuse. This is an important step because it confirms the upstream devices as well.

I would test the fuse with an Ohm meter. I wouldn't just replace the fuse. I would want to know what the fix was.

I would verify +12 volts on the TPS and IAC red wires with the key on. This confirms the motor's VPWR circuit.

I would verify +12 volts on several COP's WH/LB wires. This confirms that the ignition circuit is hot.

Best to use a test light that will "load" the circuit.

Another theory is that due to the long time this car has been setting, the PCM or the cluster has "forgotten" it's programming. In this case, disabling PATS, locksmith, or dealer are the options.

Regardless, the codes stored in the cluster will provide important clues as to why PATS is not allowing the car to start.

Good luck.

F1=BJB=Battery Junction Box; engine bay
F2=CJB=Central Junction Box; Driver's kick panel

>>Edit for completeness sake here's the information for the 1996-1998 model year
1996-1998 BJB & I/P Fuse panel layout
https://www.allfordmustangs.com/foru...fuse-help.html
Attached Files
File Type: pdf diagram-11-1.pdf (7.9 KB, 7896 views)
File Type: pdf diagram-11-2.pdf (6.0 KB, 6555 views)
File Type: pdf diagram-11-3.pdf (4.9 KB, 5689 views)
File Type: pdf diagram-11-4.pdf (6.8 KB, 5977 views)

Last edited by wmburns; 06-06-2019 at 01:47 PM.
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post #13 of 30 (permalink) Old 08-02-2011 Thread Starter
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update

I didn't have an ohm meter on me and my time was pretty limited during the weekend. But I was able to check out the fuses, all of them, thoroughly and none of them were blown.

We are now narrowing it down to the next one which is bad gas, which my buddy is suppose to drain today.

If it has fresh battery, fresh gas, no missed grounds or connectors, then the chances of it starting is even better. I didn't get to replace the fuse even though they look fine, so I should've done that when I was there with the car but the weekend was kinda hot.

Anyways that's the update for today.
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Grasshopper, replacing the gas will not fix the PATS problem. The gas maybe bad, but that's not what is keeping your car from starting.

It won't start until the theft light issue is resolved.

I make you a deal. If replacing the gas only makes it start, I will help you get a copy of the Ford service DVD for yourself.

If it doesn't start, you will have to post that wmburns is the best.

Deal?

Cluster DTC codes.
>>
Instrument Cluster Diagnostic Trouble Code (DTC) Index DTC Description Source Action
B1202 Fuel Sender Open Circuit ICM REFER to Section 413-01 .
B1204 Fuel Sender Short to Ground ICM REFER to Section 413-01 .
B1213 Anti-Theft Number of Programmed Keys is Below Minimum ICM GO to Pinpoint Test D .
B2103 or B1232 Antenna Not Connected — Defective Transceiver ICM GO to Pinpoint Test E .
B1317 Battery Voltage High ICM REFER to Section 414-00 .
B1318 Battery Voltage Low ICM REFER to Section 414-00 .
B1342 ECU Is Defective ICM REFER to Section 413-01 .
B1356 Ignition Run Circuit Open ICM REFER to Section 211-05 .
B1364 Ignition Start Circuit Open ICM REFER to Section 211-05 .
B1600 PATS Ignition Key Transponder Signal Is Not Received — Damaged Key or Non-PATS Key ICM GO to Pinpoint Test F .
B1601 PATS Received Incorrect Key-Code From Ignition Key Transponder (Unprogrammed Encoded Ignition Key) ICM GO to Pinpoint Test G .
B1602 PATS Received Invalid Format Of Key-Code From Ignition Key Transponder (Partial Key Read) ICM GO to Pinpoint Test H .
B1681 PATS Transceiver Signal Is Not Received (Not Connected, Damaged, or Wiring) ICM GO to Pinpoint Test I .
B2139 PCM ID Does Not Match Between Instrument Cluster and PCM ICM GO to Pinpoint Test J .
B2141 NVM Configuration Failure (No PCM ID Exchange Between Instrument Cluster and PCM) ICM GO to Pinpoint Test K .
B2143 NVM Memory Failure ICM REFER to Section 413-01
C1284 Oil Pressure Switch Failure ICM REFER to Section 413-01 .
U1147 SCP Invalid or Missing Data for Vehicle Security PCM/SCP GO to Pinpoint Test C .
U1262 Missing SCP Message J1850 REFER to Section 418-00 .

2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.
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post #15 of 30 (permalink) Old 08-02-2011 Thread Starter
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HAHA, I can tell you right now that you are the best wmburns, yeah I forgot, the light for pats did shut off for a bit, but then the theft light kept blinking. Didn't check the codes because of not having the info on the procedure on me to do it. I canceled my internet at home.

My buddy is at home right now trying to do it. If worse comes to worse I'm just going to send it off to a mechanic who's a friend of my friend's dad. He specializes in Ford or Domestic cars in general.
I just want to go out already and do donuts, and burnouts like a real American.

But!! to save myself some hard earned dollars instead of spending that money on a mechanic when I can save that to get a head upgrade or something, I will try everything on the list to the best of my ability.
If it weren't so dang hot here, I could go on all day working on it.

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