goofy shifting

as explained in my past posts..i just put a different tranny in a 91sc automatic
had all kinds of goofy things going on to start.. but now seems to be alittle better no reverse clunk. sometimes no clunk at all.,but now when you shift into drive if it clunks, it doesnt shift unless i drop it down into 3rd and back up to drive and it shifts great and smooth
but if it doesnt clunk when going into drive you have a great smooth shifting ride.
anyone with any ideas would be greatly appreciated my sons getting anxious to drive his 1st car
thanks