Joined: Mar 2011
Location: El dorado hills
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.