I'd suggest trying to find an OEM pair of fenders with as little rust and rot as you can find. Same fenders as a CJ-7 or CJ-5 so there is a lot of them out there. Try looking on Craiglist and FB. Aftermarket fenders don't really fit well and require a lot of "massaging" to get the holes to line up and everything to fit correctly.
As far as rubber parts, you may want to be more specific as to which ones. Cowl seal, door seals, etc. It's a mixed bag, depending on what you are looking for specifically. I am unaware of one source for a majority of the rubber parts. You could start looking at RockAuto or Quadratec.