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1979-2004 V6 Mustang Tech Discussions

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Unread 03-06-2011   #1 (permalink)
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Default 1999 mustang 3.8 Engine replacement to 2004 3.9

All, I just wanted to give some info on my engine swap for my sons 1999 Mustang 3.8L. Finding all the info was hard, so I figured I would share my experience in one place.

Summary: I just swapped a 2004 3.9L into my son's 1999 mustang. I just wanted to give as many facts and let everyone in my situation the truth on how to make the newer motor work in the older mustang.



First: When trying to get a used one I found that the 1999 and 2000 motors are differnent from the older and newer versions of the 3.8. Getting the right info was hard. I do know that these years up to mid 2000, were Externally balanced meaning the Crank, Harmonic balancer and flywheel are balanced together and there was a weight on the flywheel. This was the case up until mid 2000. Sometime in 2000 they changed the Balance to Internally and the flywheel had no off balance weight.

Second the intakes are different for 1999 and 2000 from all other years. In 2001 they introdroduced the IMRC in the intake. There are little butterflies inside the intake and a module on the back of the intake to open and close the butterflies. I have read that a lot of folks disable the IMRC due to them sticking closed.

Third: in 2004 Ford switched from the 3.8L to the 3.9L. The motors appear to be the same externally and all accessories attach fine. My understanding is that they changed the stroke 2mm and the pistons are domed differently.


So you may ask why I put in a 3.9L from a 2004. I could not find a 1999 or 2000 motor with low miles. I found this motor with only 47K. I was told it was a 3.8L and I had found that ford had switched in 2004 to the 3.9L. Once cleaning the valve cover off better, I discovered the tag stating the motor was a 3.9L.


So the route I took to make this 2004 3.9 work in my son's 1999 was the following.

1. I used the Flywheel, and harmonic balalncer from the 2004 motor. This is required to not have a vibration. Some people said to use your flywheel from the 1999 when doing this, they are wrong.

2. I switched the Lower and uppers intakes and fuel rails from the 1999 and put them on the 2004 motor. It is my understanding the injectors are different (19# vs 24# on the 2004) Could not confirm this, but fuel injector part numbers were different too. So I had to use the older Coil Pack and the bolt pattern went from four (1999) to 3 (2004). All of the smog stuff looked the same on the 2004. Only one sensor appeared different. It was the coolant temp. Moved from the Intake(1999) to the back of the head (2004). The strange part of the sensor in the head is that it did not contact the coolant. I was able to just remove it.

3. I used all the wiring from the 1999. since I used the 1999 fuel rail and 1999 injectors.

4. I used the coil pack from the 1999 as the 2004 went to a different style.

4. I used the hard heater line that goes around the motor from the 1999 due to one bend in the back on the 2004 that hit the fuel line in the back on the intake.


Installing the motor: I conteplated taking the Transmission out, but was torn on having enough angle to get everything in as one unit. I decided to leave the tranny (5 speed) in. I was able to jack the transmission up as as I could. I then lowered the motor and got the angles to match and slowly brought them together. I was under the car while my son push the front of the motor. after about 15 minutes, we got that click you love to hear. They came together. But the passanger exhuast got pinned. This caused a lot of greif and I finally dropped the exhaust. Had to disconnect all the o2 sensors to drop it.

I was able to get all the tranny bolts in from under the car with several wobble extensions.

The last thing I was worried about was the extra displacement. The computer and sensors took care of that. I was also worried about the Cam position sensor being in a slightly different position, but that was not a problem.

I tried to point out some things I had to spend a long time peicing together as one guy at a junk yard told me that I could not use a 3.9L. As I started this I was not 100% sure I could use a motor other then a 1999 or 2000. As I found out I had no real issues switching to the new motor.
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Unread 11-03-2013   #2 (permalink)
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I know this is an old thread but excellent information. My son's '99 (auto) is apparently getting antifreeze into the oil. It is slight but there is some white mayonnaise like residue on the oil cap when removed. It is not a lot, but with 192,000 miles, it's time to refresh anyway.

My question...I found a wrecked 2000 mustang 3.8 (5 speed) for a reasonable price. Is there any difference in the flywheels for a 5sp and an auto? I realize they are externally balanced so I would need to keep the 2000 intact for balancing.

Any reason why this motor wouldn't work in his 99?

Thanks all.
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Unread 11-04-2013   #3 (permalink)
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Yes there is a difference between a flywheel (manual) and a flexplate (automatic). Which to use depends what is mated to the motor (automatic or manual).

It's straight forward to convert a motor that was mated to a manual to automatic. Simply remove the flywheel and pilot bearing (IMPORTANT!) and install a flexplate. HOWEVER with the V6 comes the added problem of matching the balance.

It seems to me that you will have to take the time to determine the original and replacement V6 is external or internal balanced. This will tell you what kind of flex plate will be needed. Should both motors turn out to have the same balance, then and only then could the flex plate from the failed motor be re-used.

If buying from a salvage yard, they may be able to help get the correct flex plate for the application. Or try car-part.com for a searchable list of salvage yards in your area.

FYI, the original motor may not need anything other than a new head gasket.
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Unread 11-04-2013   #4 (permalink)
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Thanks a bunch wmburns. Found out the replacement engine is externally balanced, should be able to take flexplate off of my son's engine and place it on the donor engine.

Appreciate the info!
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Unread 11-16-2013   #5 (permalink)
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Well, in searching I have not found a specific discussion about the information I need, so this looks to be a good place to ask my question. I have an what I believe is an '85 3.8L V6 that I bought at a salvage yard in '87. It was low mileage, 18,000, to use in aviation project.

I have never finished the plane and now have a need for an engine in a 4X4 I am restoring. The need is a clutch type flywheel and a bell housing. My question is, since this version engine does not have the internal counterbalance shaft, if that makes a difference, will a flywheel have to be balanced on the engine?

I know that these engines were run in amateur built aircraft with just the flex plate. That seems to indicated the engine is balanced fairly well as the flex plates tended to crack (they were unsupported by a torque converter so tended to flutter a bit leading to cracks around the bolt circle) and could be replaced with a flex plate of of any other 3.8L and ran just fine. So, I am hoping that will be nothing significant required to bolt up a clutch flywheel ( Are the flywheels year specific or similar around certain production years?).

Also, I am going to be using a T98 (BW) transmission so will be fabricating an adapter to bolt the Ford Bell Housing to the T98. Did the engine-to-bell housing bolt pattern change between '85s and the housing used on the '94s ('94 and later BH are readily available) or are those bolt patterns the same over the years?

Thanks for any help you can offer.
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Unread 05-05-2014   #6 (permalink)
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Just wanted to reply and thank Jspires for his help in transplanting a 2003 engine in a 1999 car.

Everything he said in his original post is spot on. I would like to add that I used the 99 lower intake (because of the intake runners on the 03). However, I used the upper intake from the 03. It is a little different and required a little modification because the 99 coil uses four mounting bolts, the 03 uses three. The 99 coil needed to be used as the wiring is different and it uses a different plug. I wanted to use the 03 upper intake because I broke off one of the throttle bracket bolts and was having a hard time getting it drilled out. But the two upper's are basically interchangeable other than the coil mounting situation.

I also had to move the coolant sensor from the back of the left head (on the 03) to the lower intake (near the t-stat) to work with the 99 wiring harness.

I installed a new water pump while it was convenient.

I installed new o-rings on the fuel injectors, don't know if it was necessary but it was inexpensive.

Installed new valve cover gaskets, upper and lower intake gaskets and torqued them to spec.

Used the 03 harmonic balancer and flex plate. The 99 is externally balanced, the 03 is internally balanced.

All of the sensors (cam, crank, etc) plugged in exactly like the 99, even though the 03 uses a different crank sensor.

The car started immediately, does not throw any engine codes. No leaks, everything works flawlessly.

Thanks Jspires, I appreciate the help!
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