Rusty floors, and especially in just that area, are very common. My stepson's 93 lost a length of floor all the way from front to under the rear seat, well over a foot wide in places, even working its way up the center hump. What you do about it depends in some degree on how long you expect to keep the vehicle, what your local laws are, and how pristine you want it to be in the end. Welding in a new floor is oviously the nicest solution, and the most likely to satisfy finicky inspectors, but very time consuming or expensive depending on who does it, and in my opinion not worth it if the rest of the Jeep is old and shabby. That section of floor is not of great structural importance, and unless you cut the entire floor out you might find yourself having to repeat the job every couple of years in new spots. If you live in rust country, chances are very good that every time you look underneath, you'll see a spot that is either just newly rusted through or about to go.
What I did on the 93 was first to cut out the bad metal back to good sound stuff, and then take large pieces of my favorite repair material - old steel shower stall walls - and make plates which I laid on with a good overlap and screwed down with many self-tapping sheet metal screws. I like the small self-drilling ones with hex heads, which zoom right in with a cordless drill/driver. Both before screwing down and after, I liberally applied my favorite Vermont redneck undercoating - brushable roofing tar. The result was a tight, waterproof patch that will probably outlast the Jeep, which is now, after all, 12 years old, with well over 200 thousand miles on it.
So look carefully at your rig, and determine how rusty the rest of it is. If it's not too bad, I say go for it in whatever way you think is the least ruinous, and enjoy it. The engine and drivetrain will probably last just about forever, so if the body doesn't look too bad, fix the floors. You can always transfer the lift stuff later if you need to. But I would advise that unless you intend to make this a really carefully built, custom rig, don't put huge amounts of labor into making the floors of a 500 dollar Jeep as good as new. Make them safe and functional.
Mind you, if you really do want to do a good job, and in the process to learn a valuable skill, you might consider pricing having it done by someone else, and then use that price as the justification for purchasing a nice new wire-feed welder. The Jeep then becomes a practice tool for learning this valuable new skill. By the time you're done welding in new floors, you'll either have melted it down to a pile of crinkly rust or you'll have gotten pretty good at it. You'll probably end up owning the welder and the welded Jeep for less than a body shop would have charged to do the job, and you'll have a skill for life.
I'm only half joking here. Some years ago, I used the restoration of a rolled-over junkyard van as the excuse to buy a MIG welder. The van cost 1800 bucks, the roof another 200, and the welder 600, plus, of course, some assorted parts, glass and paint. The finished van was worth over 6000. I estimate that the day I put the roof on and welded it up, the welder paid for itself.
