Pilot bearing looks about right to me. You DO NOT want to use a dremel on it. Pull it out and slide it on the end of the trans input shaft if your feel it is not fitting correctly.
1. Did you match up your old pilot bushing with the new one? It is possible it is not seating correctly. Look in there with a flashlight to make sure it is going into the crankshaft all the way. I did have one that was too large in diameter and set it up on a drill and sanded it down a tad to get it to fit, but it has to be a snug/tight fit so it does not spin in the crank.
2. New flywheel? Which one did you use? a.) The Hays 10.5"-11" dual pattern flywheel, if you used this, is not balanced to match your engine. You may experience a vibration. b.) The Hays flywheel uses the "short" head bolts at the center hub where it bolts to the crank as it is not as deep as the factory flywheel and the larger bolt heads may hit the clutch disc springs. (Ask me how I know a & b
3. Did you replace the clutch disc and diaphram with the exact same brand/type that came out of your car? Some kits include the throwout bearing which can be wrong for a Pontiac application (another one of my experiences). I've never had any interference problems, so I don't think this should be a problem unless it is not sliding on the collar and hanging up for some reason. I would check that it slides the full length of the collar it rides on. If you install the wrong length throwout bearing, your clutch will not release properly. There is a short, intermediate, and long throwout bearing. (With the trans in position, can you move the clutch fork? Make sure it is not binding for some reason and hanging your trans up.)
4. If you know that the pilot bearing does indeed fit the end of the trans shaft, then I would measure from the pilot bushing (installed in the crankshaft) to the outside edge of the bellhousing and then measure from the shoulder of the input shaft (where the back of your pilot bushing will ride) on the transmission to the front of the trans case. You should have the same measurements. If the measurement you took off the trans is longer than the measurement you got from just the pilot bushing to back edge of the bellhousing -you have a problem, and that has to be that the pilot bushing is not right or seating deep enough into the crank.
5. If everything checks out, sometimes the collar at the front of the trans which your throwout bearing rides on, and centers the trans into the bellhousing, can be a real snug fit and can seemingly cause a problem. It fits into the bellhousing pretty tight, and maybe moreso that it is hotter in the summer and all things expand. You want to make sure it is going in square and level, any angle will add to the problem, as will the weight of the trans if it is hanging. It is best supported with a jack versus doing the "he-man muscle up and in" technique that most of us have done.
You can draw the transmission into the bellhousing using the 4 attaching bolts. BUT, IF DONE WRONG OR YOU FORCEFULLY TIGHTEN THEM, YOU MAY BREAK AN EAR OFF YOUR TRANSMISSION.
I have had the same experience where it would not go in that last little bit and used the tightening procedure to draw the trans in that last amount, but I know everything that went in was exactly what I had taken out and everything matched/fit. Never broke an ear off any of my transmissions, but it can happen. Sometimes you can put just a little tension on the bolts and then give it a shake/jiggle while pushing in to seat it that last bit.
In any case, you want to double check everything. Match your parts up and make sure they fit. Hate to say it, but if it isn't American made (and much of it isn't) the fit is not always as it should be, so check everything.