With the transmission, try to wiggle the input shaft and see if there is any play. If there is you are looking at a worn bearing which will most likely make noise once installed. Also, put a screw driver in where the shift linkage attaches with the bitch pin and slowly shift into each gear. Feel for lock outs and if it shifts smoothly. This is about all you can really do without driving it.

As for the motor, remove the valve cover and see what color it is under there. If it is like a golden color the motor was most likely taken care of. If it is dark or more brownish the motor is probably old (high mileage) or not well taken care of. Check to see if everything spins freely while turning over by hand (while valve cover is off) and check for correct cam timing. Check for wear marks on the cams. Check for "leaking" around the head gasket. If possible, pull the exhaust manifold off and see if there is equal carbon deposits in all four runners. Do a leak down test to check for condition of rings or if rings are even in there (had a friend buy a motor once off TR that was missing rings).