Yeah I probably dropped the ball on cleaning the surfaces. I had it the flywheel with some brake cleaner, but that was about it.Your flywheel and clutch cover would have been covered with a film. Did you clean that off with some brake clean by chance? I am assuming sso since you have surface rust on your flywheel that is normal. By the way looking at the pictures I don't see anything wrong especially nothing that looks like it would have been rattling.
What I do find odd though is it looks like you only have one alignment dowel on the cover and it looks like it is in a bolt hole. although that said I don't see any extra holes on the flywheel for alignment dowels. Am I looking at that right the the next to the last picture is that a dowel or a bolt?
Also I just noticed you have a crankshaft sensor eccentric on your flywheel is there any chance that was rubbing? Check that for scratches and look at the sensor. It is probably ok, but might be worth a check?
I had to swap the old pressure plate bolts out with new ones, I had installed new socket cap bolts, as one of the old semi-flanged hex bolts disappeared on me.
As far as the alignment dowels - this might have been where I was confused on the last install. There are three dimples on the AMS flywheel - I had positioned the pressure plate on the flywheel, where the three nipples on the plate stick out (thinking that was where it was suppose to seat).
There is no documentation that I can find on lining up the playe with the flywheel, so I have to figure this part out before my replacement parts arrive tomorrow.