My "new" xj, and it's multitiude of rust

Hello, first time posting here, so I guess I'll just take it from the top. For my first car I inherited by father's old 96' cherokee sport, loved the car, over 200k but never failed me when i needed it. Hurricane sandy took that car from me. Here's where I'm pretty sure I screwed up. I bought with my insurance money one that looked very similiar to mine, but a 5 speed with less miles. I didn't look the car over enough and now the problems are coming out of the woodwork. Heres a list of things I'd really like your advice with, keeping in mind I'm a broke college student (who really got himself in a pickle).
1. rockers and floors are rusted through
2. rust spots no bigger then a baseball (four where an aftermarket roof rack held the water) on the roof by the gutters
3. the driver's side seat bolts to a piece of metal that runs between the uni-body "frame rail" and the rocker (which isen't rusted to bad there) is cracked, I'd love to know what to call this, many a google of seat bracket and seat support did not come up with it.

I am not a mechanic, but many in my family are, one has a garage and can weld in new floorpans/rockers when the time comes.

It's a 1996 sport with the 4.0L six and the five speed (ax-15?) manual, I don't know the front but I'm fairly confident it's a Chrysler 8 1/4 rear axle with a 3.07 ratio, I'm not sure how this would be relevant to body work but I'm being thorough.

I'm fairly certain I'm going to use rust neutralizer on that roof, then rhino line the entire roof, for now I've rust neutralized and jb weld apoxy'd to get me through the winter. As far as the floors and rockers, I hope to get some new sheet metal and put it in this summer at my uncles shop. The reason I'm posting is to find out about any semi-permanent solutions that are out there. I just discovered the busted seat mount/support thing, and that's by far what concerns me the most, would banging that bracket back into place (its bent less than inch) and jb welding it be safe, what else could I do. As I said, not a mechanic, but I no more then most Any help with the repercussion's of letting my heart make the buying decision and not my head would be greatly appreciated. I'd like too keep the Jeep, I've always wanted a five speed and the motor runs like a song, as far as drive train there are no problems so far.

Jb weld on anything structural is a terrible idea. Id look into turning a few of these problem areas into "upgrades". for instance, the rockers being rusted out... cut them out completely and do some 2x6 steel for sliders/ rocker protection. The floor, well you will have to do the floor pans, if you can't weld you can air craft rivet and use seam sealer to put small panels in, anything large I would suggest welding in place.

But put the jb weld and bondo away, if you want professional looking results you will have to learn to do some metal work, if its as bad as your saying...

forgot to mention I'm also planning to rhino line the rockers and floor pans once the new sheet metal is in, btw has anyone used classic to current panels before, they offer about the cheapest prices and they sell the front and back of each side as one piece. I don't think it will matter if they are a bit thin, because as I said I plan on rhino lining them, I've heard its just about the best rust proofing around, if you don't mind the rough texture, which i don't. As far as that seat bracket, I'm not talking about a permanent solution, just something to get through the winter, but if there is no such thing, perhaps I'll have to keep gettin' rides til the weather warms up and we can redo those floors.