Trying to get clutch disc alignment close enough to get the transmission to slide all the way in with most “alignment” tools can be especially frustrating, especially when using those cheap plastic ones often supplied with the disc. Even loosening and retightening the pressure plate multiple times won’t get it done at times.
I’ve had far better luck using an actual input shaft from a transmission. It just needs to match the disc splines and register in the pilot bearing correctly. While I prefer the weigh and “feel” of one that isn’t broken, a damaged one will work as long as the splines and pilot bearing area are unhurt.
“Wiggling” the shaft as the pressure plate was tightened seemed to help, but it was likely my imagination.
O T, but I tore up so many Muncie 4 speeds “back in the day”, I still keep a shaft from one of those in my toolbox.
Engaging two gears at once will lock the transmission and allow rocking the case around the main shaft axis to get through the disc splines if that is an issue.
I’ve tried all the tricks mentioned previously, and few more, usually with little success. Multiple tries of loosening/tightening the pressure plate to readjust the disc, with the attendant removal/reattachment of the bellhousing and attempted reinstallation of the transmission, frustrating as that can be (especially if you are laying on the ground bench pressing a 130+lb transmission into place), was usually the way it got done.