How about crank to transmission runnout? Different trans housing could introduce mis-alignment. This is usually a manual trans issue (I have had it!) but can also affect autos... especially when parts are swapped and especially if the engine was line bored.

On an old power wagon (not put together by me) misalignment was enough to crack the clutch pressure plate, wipe engine main bearings and transmission input bearing. The symptom (besides eventually low oil pressure) was a light metallic noise from the bell housing caused (I believe) by the crack in the pressure plate moving.