Cheapest tranny fix would probably be a straight out swap, as they can be had for about $2-300. You're looking for an AX-15 to mate to that 4.0 engine - the AX-5 tranny is for the 2.5 4cyl engine.
Seats - easy swap.
Floors....cut and weld in new metal. Only REAL fix for that.
Go to a dealer and you will pay a lot for fixes, but really learn nothing. Spend some time talking to jeep guys, visiting them, and offering to help them out in exchange for info, and you'll learn more than you ever thought.
