After measuring and checking the entire trans out, I did find that all of the front clutch steels have a small spot of heat scoring in one area. The clutches all look fine, but every steel has this scoring in the same spot on the clutch stack almost like something is bent or high. Everything checks out flat so far, and the clearance measured to .045". That is tighter than spec, but I am running 5 clutches in the 4 clutch drum. I'm not sure what the cause of that is, but I doubt it is coincidence since my car slams into reverse and 3rd gear and the front clutch is engaged in both of those gears. I don't think it is related to the flexplate problem, but the harsh shift was another concern I had.
Also, is there supposed to be a metal washer or race on top of the #3 thrust washer that goes between the input and output shafts? My end play was in spec, but for some reason I remember there being two washers on the end of the input shaft of the LU 904 I tore down. I only have one fiber washer. I don't think anything fell out when I tore it down.