The Nissan Path

I have a 1995 Pathfinder that I got from my girl friend, after she blew out the transmission. I replaced it with an auto from a later model, but now it won't shift into drive. If you drop it in to 1st, or 2nd it will drive fine. It is weird because transmission was pulled from a running and driving pathfinder. I want to figure out the shift problem before winter hits. I also installed a 3 inch body lift to make the transmission swap easier. I plan to add a suspension lift of some kind, a huge transmission and oil cooler, and some exhaust headers. I would post a pic of it but I don't know how.