I finally got home and had a chance to take some measurements. The TR2 through TR3A input shaft has a mainshaft bearing ID of .91" The TR3B-TR6 early has the hole for the needle bearings that is 1.12".
Of note, the bearing surface of the mainshaft is the same size for both. So...it appears the input shaft for a TR2/3A will work with the TR4 box, so long as you use the bushing instead of the newer needle bearing. I would imagine the TR4 input shaft will work backwards to the TR3 also, so long as you use the needle bearings.
This may become important, as the later input shaft is becoming scarce! That seems interesting to me, as there were a lot more cars with the later shaft built. I guess those cars are getting rebuilt more frequently than the earlier cars?!?