cjman, have you actually done this before??
in order to get that steel bearing input shaft retainer on, the transmission does have to come out, however, the tranny slides right out, and the bell housing, clutch fork, and clutch do NOT have to come out.
however, I'll bet the farm that that's not your problem. Your clutch adjustment is slipping for some reason. do you have an adjustable cable or a firewall adjuster? If you have an adjustable cable, your adjustment is loosening up at the fork, if you have a firewall adjuster, its backing off and loosening there. If that is not happening, your cable is stretching. What is your exact setup right now??
it is very common for throwout bearings to squeak when not enough preload (pressure) is on the pressure plate. The mustang clutch is designed to have a constant amount of preload. You need to adjust your clutch properly which will take care of the squeak. In fact, with it set right now, it's a little stiff getting into gear, and it picks up right on the floor. all of this will be fixed with a simple adjustment.
http://50stangs.com/techarticles/clutchcableadjustment.html
I wrote a really good article on all of this. You need to read it. Adjust that clutch properly before ripping anything out.
if you can't get your adjustment to keep from slipping on you, get back to me and tell me exactly how you are set up, and I'll help you get to the bottom of this.