How to remove a tranny input shaft?

[Ralph Moore]

A friend's mating a 1967 Mustang four speed to a Y block, the input shaft needs to be shortened about 1/2"(rough measurement) at pilot bearing end. I went over to help him take it apart, and after we had the throw out bearing sleeve/cover off the bearing and top plate off tranny, I thought the shaft would come right out, but it moves about 3/8" and won't go. What's holding it?
Do we have to dissasemble the entire tranny?
I don't remember doing that on my 3 speed.