If your going to use a automatic tranny with a stock type or race converter I wouldn't worry too much about it being dead nuts on input shaft to crankshaft center line due to all the built clearances in the front pump and flexplace centering the converter to the crankshaft center.
If the converter will slide into the back of the crankshaft easily installed in the tranny with the tranny hooked up to the motor and the converter bolts install easily, I would use it the way it is :: up: