Jus recently had an engine swap, have a 99 manual gt and had an 04 gt engine placed in my car. and now ever since the swap the engine seems to shake at idle and upon the low rpms while accelerating?
It is possible that a coil-on-plug (COP) is weak or gone kaput. This *should* put a code up.
Do you have access to a datalogger? It would be interesting to know what the idle speed is and the commanded idle speed. It is possible that the '99 IAC table is different than the '04 IAC table and this could be contributing to the problem.
ruled out all the little things, nothing.
Thinking maybe its the flywheel since they are different from the 99 and the 04
i think that the 99 had a 6 bolt and the 04 an 8 bolt. Correct me if im wrong.
The flywheels on Romeo modular 2Vs were 6-bolt. In 00 when Ford had to use Windsor mods due to a fire at the Romeo plant, truck 4.6s were put into Mustangs. These were 8-bolt cranks. These flywheels are not interchangeable but only because the flanges are different. The mod is an internally balanced engine meaning the flywheels and dampers are neutral balanced. IOW, the flywheel is not likely the problem.
Early mods had a 10.5" clutch. Later (2002+) used an 11". Q: When you installed the clutch, did the flywheel have the dowel pins for the clutch cover?
The flywheels on Romeo modular 2Vs were 6-bolt. In 00 when Ford had to use Windsor mods due to a fire at the Romeo plant, truck 4.6s were put into Mustangs. These were 8-bolt cranks. These flywheels are not interchangeable but only because the flanges are different. The mod is an internally balanced engine meaning the flywheels and dampers are neutral balanced. IOW, the flywheel is not likely the problem.
Early mods had a 10.5" clutch. Later (2002+) used an 11". Q: When you installed the clutch, did the flywheel have the dowel pins for the clutch cover?