skyhiranger.
I was thinking what if I just pressed the pilot bearing a little further into the flywheel? Not pressing it so far that its not in full contact with the flywheel.
A stock pilot bearing doesn't "hang out" of the flywheel much with one side flush with the flywheel. So to keep a stock pilot bearing in full contact with the flywheel, you don't really have much "tweak" area.
One thing to consider is that with the thicker plate between the tranny and engine the tranny input shaft doesn't sit quite as far into the center of the flywheel (pilot bearing). So you don't want to push the pilot bearing in so far so only like half the tip of the tranny input shaft is in it. Gonna be hard to say how deep you can go with the pilot bearing and still have the input shaft positioned properly in it.
I can tell you with just a regular stock metal plate between the tranny and engine that I had to bottom out the wider pilot bearing against the crank (start the pilot bearing in the flywheel, bolt the flywheel up to the engine, then bottom the bearing out against the crank), to get it deep enough so the pilot bearing stayed on the machined part of the tip of the shaft. I checked input shaft to pilot bearing engagement by putting a dab of grease on the tip of the input shaft, sliding the tranny and engine together and bolting them up, then taking it all back apart and seeing where the "engagement line" was in the grease.
So if you wanted to use a wider pilot bearing, and since you have the thicker plate between the engine and tranny, I would guess you could probably set the pilot bearing flush with the engine side of the flywheel and be about perfect. But I don't know how close the tolerances are on input shaft to pilot bearing engagement, so I can't say for sure.