Thank you all for the answers, and for the correction on the trans.
What is the proper way to test the harmonic balancer to ensure that it is in proper working order?
I wanted to know everyones thoughts since the trans is actually a M5R2 instead of a T5, would the flywheel I chose for it (from the 3.8L) be the correct weight or could that be an issue? What weight/tooth flywheel should be on there?(The one from the 3.8l or a manual 5.0 one?)
Also, could anyone give me the flywheel weight/tooth that would be in a natural 89-92 3.8L SC 5 speed?
This might be your problem: an imbalance mismatch.
Your 5.0, unless you downgraded it to a crank from <1982, will need a 50oz imbalance flywheel.
* 1997 to 2000 mustangs are externally balanced 28oz.
* the later Mustang V6s from 2001- ’04 have zero balance. All mustang flywheels are fitted with 164-tooth starter gear rings.
* The very first 3.8L SCs from 1989 had a 28oz imbalance (and cast cranks, etc).
* SCs from 89.5 or 90 through end of production (95) were neutrally balanced.
I did the research for my swap. See this thread
Since it sounds like you have found a starter+clutch+flywheel combination that works for you, you COULD rebalance the flywheel you've got for 50oz.
Or, you could go the 1995 F150 5.0 route.
In my situation, the only thing I needed to do was clearance the scattershield a little bit because there was a slight lip to the starter where it meets the shield that was a slightly different diameter on the F150 scattershield. The actual starter position is done with the mount bolts so the actual shape of the hole in the scattershield doesn't matter.