Hmmm. When you removed it before did you move the clutch disc for any reason? Loosen the pressure plate or get in the truck and push in on the clutch pedal while the transmission was out of the vehicle? If you have the clutch disc lined up with the pilot bushing properly, the transmission should slide in just right. If you don't the input shaft can hit the pilot bearing rather than going in and cause a problem like you described...but usually you'll only be an inch to inch plus 1/4" shy of going in. If you don't have a disk/pilot bearing tool (most today are plastic), you can loosen all the pressure plate bolts until you feel the clutch disc is free to move and then install the transmission. You'll just need to move the disc with a free finger as you stab the hole and then move the transmission until you engage the pilot bearing.

~ Jon
1952 1/2 ton with 1959 235 | T5 with 3.07 rear end