The pilot "bearing" was actually one of the easiest parts of this job, partly because it wasn't even a bearing. I suspect it used to be a bushing (some people like to replace the bearing with a brass bushing), and it looks like it got chewed up pretty bad. Not even close to the same ID as the new pilot bearing, which fits nicely on the input shaft. Didn't even have to take apart the bearing puller to get the teeth it, since the ID was so large...
Probably one of the sources of my vibrations. It came out with about 5 whacks of the slide hammer. The other source for my clutch troubles was probably because the clutch that was in there was trashed. Missing springs, broken spring pieces falling out, clutch disc was almost worthless. Flywheel had hotspots, didn't look good. I'll have some pictures of that tomorrow. I'm not sure if it was previously installed incorrectly, or if it was beat on by the previous owner, or if it was just a bad clutch or too many miles, but it looks bad...
The hardest part of the job was actually getting the bellhousing off. The bitch was stuck to the motor, the pins that help line it up just didn't want to let go. Took a half hour of banging with a mallet (and triple checking for more bolts that we may have missed) to get it off. We greased the pins before putting it back on.
All in all, everything went pretty smooth. We have about 5 hours into it so far, but my buddy had to leave for a birthday party so we got cut short. We got the new clutch and pilot bearing in, new slave put in, remote speedbleeder put on and routed to the engine bay, new adjustable master cylinder installed, transmission hooked back up, and hydraulics bled. All that is left to do is reinstall the torque arm, transmission crossmember, exhaust, put the shifter back on and put the console back in. Then adjust the master cylinder and possibly rebleed, we'll see.
Edit - You can't pack anything behind the LS1 pilot bearing because the crankshaft freeze plug is right there, and can pop out and drop into the oil pan.