I bought an old CJ and joined these guys:
On the floor pans, they are very easy to repair, so you really won't (shouldn't) need a Jeep specialist. Without seeing them, it could be a repair where:
- patch panels (sheet metal) is cut to match, grind out the old and in with the new (welded or riveted and sealed)
- new OEM panels are put in where the rotted ones are now. Cut to fit, paint to match
It just depends on what your expectations are for the Jeep. Are you wanting to fix for safety/DMV sticker or are you wanting to fix it up "nice"?
NOTE-*DEFINITELY FIX ANYTHING THAT WOULD ALLOW EXHAUST FUMES INTO THE CAB, IF YOU ARE RUNNING A ROOF!!*
If it's not you daily driver, maybe someone who can do it "on the side". My CJ passes inspection and is NOT my daily driver. The floors are rusty and have been patch paneled. I just drive it and have fun.
Maybe check CL for tires/rims....there's always lots of Jeep stuff listed.