Might be worth checking the TDC mark to make sure the ring hasn't slipped.
Only other thing I can see that might be off is the TC. You said you had a shop build you one, is it possible that it never got balanced to neutral? I know you said that was what you asked for, but could it maybe have missed the balancing step?
It's the only thing I can think of outside of the motor having been balanced in it's past at some point and now the stock weights won't work.
