is it possible something went awry on the engine install with regard to the transmission? torque converter hub not seated properly, torque converter not engaged properly, kick down or linkage not attached properly, a bent or kinked line?
and maybe one of those instances were already at work, and changing the fluid & filter just happened to be a coincidence with the problem you're currently having.
I can't see how the pinion leak would have any effect on transmission operation.
