You probably just got air in the fluid lines and/or in the torque convertor. You did put in the spacer required for the deeper sump, didn't you? It just spaces the pump filter down a little lower into the new pan so that it will be able to pick up fluid. Did you put a little bit of blue locktite on the threads holding the filter on so the bolts wouldn't back out?

Automatic transmissions don't go bad just because you swapped the ATF oil pan, and it sat for a little bit.