On my 3A, the drivers seat also bolts through the rear wheel well. Mine has a nut welded onto the seat frame and a bolt through the wheel well, but I can't remember if that is factory or not. Part of me is thinking there should be a stud on the seat frame that fits through a hole in the wheel well with a nut to secure it.....
Like you, I had a repo tub and had to make numerous mods for it to work. On the passenger seat, my support bracket on the wheel well is too far down and doesn't really support the seat. I found this out after paint......even after putting the jeep together prior to paint.......twice. I simply split a piece of radiator hose and fit it over the cross bare on the back of the seat than mess with moving the support bracket.
There are sooooo many little things that might be wrong with a repo tub you will miss a few no matter how careful you are in trial fits. Your problem with the fuel sending wire made me cringe a little bit. I had the exact same problem and didn't realize it until I installed my wire loom. At that point, I had made so many little fixes on the repo tub I just cussed a few words and drilled a hole where there was supposed to be and forgot about it.