Couple of ideas here. First of all…metal is intimidating but when you get right down to it, it’s more forgiving than wood. You can always put metal back on…try that with wood. Anyways, I agree that the original body and frame are the heart and soul of the vehicle. So if you can keep them, you’re ahead of the game.
I have a boat deck hatch that you’re welcome to. It’s brand new, about 12”x14”, and it’s made out of black poly. Heavy duty. My bed floor was pristine or I would have used it myself. So there’s that.
Widening the area between the wheel wells. The rear axle travels in an arc, in the direction of the shackle. That’s one of the reasons the stock mount was angled back. If you took Sdudpilot’s idea and angled it towards the rear like stock, you could gain width over the majority of the wheel well. Maybe just a box like area at the back for the shock tower. Also, look at the wheel wells from a 72-73 commando. They have an angled area towards the top for more seat room. Remember- the seat doesn’t sit flat on the floor, there’s room to play with.
I can’t recommend a LS swap enough. But probably not enough to get you to do one.

I can’t think of anyone who has done one and wished they hadn’t. You want reliability and power from a platform that provides all you need in stock form? LS, baby.
If a LS swap seems wrong because it’s not Jeep, then do a Hemi. It’s not “Jeep” either but at least it’s been used in Jeeps.
Face it. You need to do this at some point. I know your reasons for wanting to try and limp through for one more year- but if we’re honest, it’s the people and the relationships that make the events. What you drive isn’t as important as the memories made with friends.