I read your old post from 09 linked above. It looks like you didn't have the problem, replaced your flywheel and your cracked bellhousing with a new one, and had a problem. BUT it didn't vibrate without the transmission installed. Did I follow that correctly?

If that is correct it really sounds like, even if you did index the bellhousing, it wasn't indexed correctly and you had a serious input shaft/crankshaft misalignment, causing your vibration and this eventual carnage. Do you recall what the runout was when you indexed it?

Why did you have to trim the input shaft?

Now I need to pin those needles, got to feel that heat
Hear my motor screamin while I'm tearin up the street