Well....damn.
Got the hatch hinges loosened, and I snugged the hatch tighter. It is now flush with the rear of the body. Looks good. Slid the pin out as far is it would go, and it grabs the catch and hopefully won't rattle the pin now (have to see on that one.) If not, it gets welded. The rubber seal is compressed tighter than it ever has been, so this may help things. I thought I'd have to shim it too in order to keep it from dragging (per Grimm's suggestion) but once I moved the hinges up the body big-time, I didn't need to raise it any. Nice 3/8"-1/2" gap all evenly along the bottom now...no dragging or scuffing of any more bumper paint.
Roof rack: pulled everything off. Tried regular well nuts in the holes for the OUTER two rails, but they won't do the job. The parts that I'm replacing (due to 20+ years on them) are best described as threaded rubber grommets to my eyes. Look like a donut with a horizontal groove in them, which is where the sheet metal roof pops in. Threaded down the center to hold the bolts.
Jeep wants....ALMOST $6 EACH FOR THEM! x 12!
Can't seem to find anyone either online or locally that sells these damn things. Not Home Depot, not any hardware stores, not any automotive stores, not NAPA, not Grainger...no one. Was hoping someone here had some ideas on where to find them.
On the inner smaller rails I tried regular well nuts (had to drill out the holes a little bigger in order to fit them though) and new screws and generous amounts of gasket maker. On all the rails I'm trying regular rubber grommets in the holes in the actual rails as well. I hope these regular well nuts will hold/work/tighten for the smaller inner rails...I'm waiting for the RTV to cure before I try them. If not, I may see if I can get threaded rubber grommets for these smaller holes as well.