First of all anything could be wrong with the the trans., who did the rebuild, done correctly? Look for an improperly seated main plug on the trans. A full trans scan can command those solenoids and check if all the connections are in place. Second, look for a pinched harness somewhere in the headlite/tailite circuit, maybe something done when the drivetrain was in and out? The engine performance, again many things can cause this, a full scan will look at sensor inputs, fuel trim and any other controls that affect mileage and performance. Can we assume none of these issues were there prior to all the work being done?