Ram running rough

My father in law has a 96 dodge ram 1500 and it seems to be running rough going up hills or when the engine is under a load every now and then it starts a little hard. When going up hills the 4x4 shifter will shake really badly when it is in OD when he takes it out of OD it seems to get better because the engine is not as much under a load, the check engine light is on. He changed the plugs, wires and distributor and still no help, so he took it to a mechanic to do a diagnostic witch cost him $80 and the mechanic said that it was the plenum gasket under the intake. My father in law the truck home and changed the plenum gasket and that still did not help. Now he is thinking it is the transmission and I have to disagree, I could be wrong but I would hate to see him change the transmission and that not being the problem. Any suggestions on what else he could do before he changes the transmission.