I dropped the transmission with the slave still attached. It seemed to be in the right place in the release lever.
Sorry for the poor photo, but this shows the clutch disk with a bit of scorching near the the fastener. This probably occurred while we purposely made the noise on the lift.
This is what the pressure plate looked like.
The throw out bearing that I installed was for a 987 (pelican said this was the only one they sold) and I had to buy a new ball pin and release lever for it. This is the old OEM 986 pivot piece that was in there from the factory (or last clutch job). I left it in even though the new release lever didn't seem to have grooves for it. Maybe that was a mistake?
I still don't know what was causing the problem, and am not sure if the clutch disk is still good... Not really sure how to proceed here.