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Hey guys, I have an 04 Mustang with the 3.9.

About two months ago my car started misfiring/Jerking when I press on the gas/accelerating. Code read: misfire randomly. Then few weeks later heard screaming coming from the hood. After long hours of research via internet I found the problem with the annoying noise, after replacing the Water pump, pulleys, belt, then... the Synchronizer. Anyway I get a new one from O-Riley which came with the new sensor included. I had talked to a mechanic prior to trying the install and he told me that I could mark the locations of the old unit and line everything back up exactly to avoid my concerns about not finding exact TDC.
The noise went away, but the misfiring did not (Hoping that would cure both). Then after I replaced the Synchro I got the P0340 code. Figured I put the thing in wrong, but still ran the same before I replaced the Synchronizer. Then replaced all spark pugs, and wires. No Change. So maybe two problems at the same time?

Now its not showing any codes. Not even a misfire code anymore.

One thing I forgot to mention; the new sensor that came with the synchronizer would not plug into my wiring harness. It looks almost identical, both are two prong, but the male connectors on the sensor are just slightly larger than the female connectors on the harness. Instead of altering a bunch of stuff I just used the old sensor since it was the bearing of the synchronizer that was bad. Any ideas would be tremendously appreciated. Sorry for the length of the post. Thanks.
 

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Have the alternator tested for a bad diode.

Double check the spark plug wiring routing. Have all factory standoffs and looms been used? Are the wires touching any metal parts?

I still recommend checking the cam syncro alignment with the correct tool as recommended by Ford.
 
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