I recently bought a 98 XJ with 93,000 miles. I knew it had some rust in the drivers floor pan and starting on the rockers. As part of my efforts to install Bushwacker flat fender flares, I found two areas of substantial rust. I know cutting out and rewelding is the best approach and some may require that. I'm building a budget driver / trail rig so showroom appearance or full restoration isn't a priority. Basically I'm looking to stop what rust I can and repair (i.e. cut out / reweld) only what I have to.

98 XJ with 4.5" lift and Rubicon take-off rims/tires
Let's start with the rockers... the rear of both rockers are starting to bubble and the passenger side has a hole about 1/4" in diameter. The metal around the rust hole and bubbled area sounds / feels pretty solid with the "knuckles and fist" test. I bought some black push-in style plastic plugs from the local hardware store. I bought four 1" plugs and eight 1/2" plugs. My plan for the rockers is to drill a 1" hole to (hopefully) remove the rust around the small rust hole. To satisfy my OCD ;0) I would drill a matching hole at the same location on the front of the rocker as well as the same on the drivers rocker. I would also drill four 1/2" holes evenly spaced on the under side of each rocker. Buy Eastwood internal frame coating and blast the inside of the rocker in the 6 holes I created in each rocker. I would then sand the rocker to remove what is hopefully surface rust and prime / bed liner. I realize rockers may be rusting from the inside but for $25 I'm guessing I can get several more years out of the rockers (and maybe forever if I don't drive it in Northern Wisconsin's winters) and it should look pretty good. I could pull the plugs a few times a year to see if any moisture needed to drain. Thoughts on this approach?
Passenger Rocker
When I pulled the rear bumper covers off I was afraid I would have the dreaded XJ fish bowl and on the passenger side I found a hole under the cover. While I was thinking about doing the same "drill out rust (hoping 2" hole saw and 2" plug would work?), coat with Eastman's internal frame coating and install a plastic plug" approach, I am afraid that when I cut the rear quarter to fit the Bushwacker flat fender flare that I might be cutting right through the rust hole so a plug may not work. When I cut for the flares if I can't plastic plug I will see if a friend of mine can weld in a patch after I coat the interior of the corner. I don't want to do the rear corner fold in part because I already have my flares and they are for the "non-folded" rear corners. Do people drill holes in the bottom of the corners for drainage? If so are the holes normally plugged and plugs pulled to drain or just left open? Again, any advice on the corner repair would be appreciated. I may just keep the rear stock bumper with bumper end covers so they would cover up any plugs / repairs I make in the corner.

Passenger rear corner
My biggest surprise was when I saw that the battery tray has completely rotted through including the inner fender. When I do tackle this it will need to be cut, form some metal and ask someone to weld. I looked but haven't seen patch panels or new inner fenders available. Anyone have any thoughts on how to tackle the battery / inner fender repair?

Rusted battery tray
Lastly is the infamous drivers side floor plan. I knew there was some rust starting here but the previous owner appears to have done some fiberglass repair then bedlined the front 2/3rds of the interior (everything but rear cargo area). Debating if I should just POR-15 from underneath and see how long it lasts or if I should start peeling back rusted metal and "dive in". Thoughts?

Drivers side floor from under vehicle
Thanks in advance for your thoughts and advice.

 

I just went through this with my jeep. My rockers actually looked way better then yours. A couple passes with a wire wheel on an angle grinder revealed what I was hoping not to see. (Holes) My rockers rusted from the inside out, hopefully yours didnt. If you can get down to clean metal on the outside, I'd exopy primer it, then paint to wanted color. As for the inside I also drilled holes and used the eastwood internal frame coating. I'll hope it works but without being able to knock all the rust loose and get it out of the rocker I'd be skeptical. Hopefully it just slows down the inevitable.

 

Looks like mild rust, easy to replace with a cheap welder and a good learning skill

 

Well I cut about a 3" square hole out of the rear corner so I guess I'm going to learn how to do some patch repair. Have a 110 wire feed I can borrow. Thankfully the inner rocker and rest of the rear passenger corner don't look too bad on the inside. A little POR-15 after cleaning, weldable primer and a patch and I should be good. Thankfully my first attempt at real body work will be covered with the rear bumper cover or if I go with an aftermarket bumper I'll get some armor to cover my handy work.