I have a Ls3 with and fbody t56, clutch, flywheel and the input shaft bottoms out on the pilot bearing about 1/2 to 3/4 inch before the trans meets the bell housing. I applied a small amount of grease on the input shaft to see if it contacted the face of the pilot bearing to verify this is in fact the issue. Is there a pilot bearing out there that sits deeper in the crank? The pilot bearing is from gmpp.

 

There are 2 different pilot bearings, a google search will tell you more as I can't remember off the top of my head. I ran into the sa,e issue about not wanting to mate together. I work on cars for a living and never usually have issues mating engines and transmissions together but mine was a pain in the ***. I ended up getting it finally just the right combination of wiggling and turning the driveshaft in the real of he trans to get the splines to engage.

 

Are you sure it's the pilot bearing that's the issue? I do recall there are different pilot bearings depending on what you have, but thought it was diameter of the shaft - I could be wrong.

If you are that close, but not able to mate the trans and bell then it could be your clutch slave cylinder doesn't have enough clearance with the clutch fingers - a problem I had. It's easy enough to measure the clearance at the clutch and then the clutch slave and then see if that's what the problem is.

 

apparently there are two styles of pilot bearings, roller ball bearing style the came in ls2, Ls3 &ls7's and the needle bearing style that came in ls1 f body's.
the needle style sits deeper in the crank which is necessary to clear the longer input shaft from a ls1 fbody t56. I just ordered the needle bearing style.