Welcome to the board, and hope we can help. I would suggest looking at what has changed in the engine, rather than assuming that an existing part like the transmission or torque converter went bad. A couple questions:
-You said the rods were weight matched, but was the reciprocating assembly also balanced? The new pistons probably don't weigh the same as the old pistons, and the crankshaft would have to be re-balanced to match the new piston+rod weight.
- The nose of the converter has to fit into the crank rather precisely. Was there any change in the crankshaft that would make the rear hole of the crank larger, so that the converter wouldn't fit into the back of the crank precisely?
I don't think that the runout measurements on the flywheel or crankshaft are a problem, although of course you would like to see those as small as possible. It seems that you are bending the flexplate a little when you bolt on the converter, you could try to use some shims between the converter and the flexplate to keep the flexplate straight.