The background: Recently completed a T-5 swap into my AOD car. Bought a used T-5 from a friend of a friend that supposedly came out of an 88 Saleen with about 80,000 miles. Installed with aluminum flywheel, King Cobra clutch kit and a used FRPP aluminum driveshaft that came out of the same car, though supposedly with less than 10,000 miles on it. Drove the car, HATED the way the clutch engaged and the low speed driveability with the aluminum flywheel. Also, and this is the problem I'm seeking help with, there is an incredibly violent vibration under load in 4th gear. So, I swapped out the aluminum flywheel for a new cast iron one and reinstalled the stock driveshaft, thinking that perhaps the aluminum one was out of balance or had a bad U-joint. The cast iron flywheel cured my problem with clutch engagement and low-speed driveability, but the same vibration is there in 4th gear. The shifter handle vibrates so violently that you almost can't grab and hold it. Also at 95 mph + in 5th, there is a deep, thrumming vibration that seems to increase with speed. Other than the vibration, the thing shifts smooth and crisp and makes no noise at all.
My assumption here is that the bearings in the tranny are FUBAR. Any other educated opinions?