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?