This is where your "free" CJ starts to cost you money
...the majority of the floor pan where the seat was mounted (or at least appeared to be) is rusted away. If i replace the floor pan, will this fix my problem? Also will i need to replace any other mounts or support bars of any sort?
My advice is that you won't know the full extent of the damage until you pull the tub totally off, or start disassembling things (seats, seat belts, console, roll bar, etc) so you can get a good look at the metal in the problem areas. I would bet money that the diamond plate on the sides is there to hide rust.
As far as repair, it depends on how much metal restoration you want to do (or pay for): Some folks will scrap a tub that has major rust in the usual spots, but some folks will take the time to weld new metal into a tub that is full of holes all over the place. If you have to take the route of a replacement tub, there are options from a better CJ tub, a YJ tub, a new or used fiberglass tub, or a new metal tub (not cheap).
As far as repair, you can buy replacement sheet metal panels for the rust-prone areas. There are thin/cheap options and thicker/more expensive options. Or you can buy 16 gauge steel sheet and fabricate your own replacements. Again, people go different routes here.
Please just don't slap in some roofing flashing, bondo, plywood, cardboard, or rivets.