1997 Hyundai Accent Changing the clutch

Recently I purchased a 1997 Hyundai Accent, it has the 1.5 4-cyl. Engine and manual trans, The clutch was out of it, so I bought a clutch kit, took the trans. Off the motor and changed the clutch, putting it back together is a pain, I have ever thing lined up, even used the clutch plate line up tool, but can't seem to get the trans. Back into the motor, it lacks approx. 11/2 in. To be put together. A friend told me to take back apart and see if the brass bushing that is in the middle of the fly wheel going into the motor has a bur on it, also that the end of the trans. Shaft, that goes into the brass bushing looks ok. I looked at the end of the trans. Shaft and the shaft has splines all the way down it and there is no small part on end to go into brass bushing, I see nothing broken off. Is there some thing wrong? Does this trans. Shaft with the splines go into a brass bushing in the motor?