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A cracked flex plate will make a ringing sproing type noise @ start up - hard to describe unless you've heard 1. Noise will be loudest when the starter dis-engages.
Put it up on jackstands and put it in drive and see if you can figure out where the vibration is coming from. It could be an out of balance driveshaft, it doesn't necessarily have to do with the transmission swap (although to be honest, it seems likely). But I don't know offhand what you could have done that would allow you to drive the truck around but have a bad vibration.
Where did you get the converter and flywheel from? Are you sure you're using the right imbalance on the flywheel?