Did you remove the clutch. Normally when it won't go back in the clutch disc and pilot bearing are out of alignment. I have a bunch of used input shafts I use for clutch alignment tools; they work better than the old wooden dowels they sold. If you replace the pilot bearing, clutch disc and throw-out bearing always make sure they slide onto the trans first before installing them. That way you know for sure they fit and you're just fighting an alignment problem and not a wrong part. Every once in a while, at work we would get a trans that despite everything being lined up just did not want to slide in. What worked really well was disabling the engine so it could not start. Hooking up a remote starter switch and cranking the engine while you shoved on the back of the trans. If you have a helper have them, get in the car and crank the engine while you push on the trans. Just make sure that engine cannot start. They usually slip in doing that. Kens alignment dowels are a good idea. I used to cut the heads off of long bolts and then grind a chamfer on them When I was young and working on the ground at home, I used them while trying to bench press transmissions back up in on my Mustangs. It was nice to be able to be able to stop and take a rest with the trans on a fl started on the dowel pins. Now that I have a hoist and a trans jack at home I can take my time and look around the bellhousing to see that I have an equal space between it and the block. The trans jack lets you make all kinds of little angle adjustments. If it's not a perfectly lined up it won't slip in. Make sure you have the same spacing all around that bell housing, so you are not trying to put it in at an angle.
