It is always prudent to replace the flywheel pilot bearing when ever you have the engine or transmission out of the car. However many people ignore the condition of the pilot end of the transmission input shaft. Many are worn down from spinning inside the bearing. This condition aLLows the end of the shaft to be improperly supported and leads to popping out of gear.
The end of the pilot shaft should have a nice "sliding" fit into the bearing. You do not want an interference fit as you would have difficulty installing the transmission.
Input shafts pilots can be repaired. I have a friend and colleague who has a Model A shop that has developed a repair technique. He turns down the pilot, then presses on a sleeve with an interference press fit, then turns down the sleeve for a "sliding" fit into a new bearing.
His price is very reasonable. If anyone is interested contact Jim's Automotive Services, Costa Mesa, CA 714-546-2969.
Tom Endy