update:
I pulled the headliner today. And, after getting it out, I'm really surprised. I initially decided it had to come out b/c the LAST row of bolts that runs across the rear of the roof, right by the hatch, had water dripping off the bottom of the bolts on 2 or 3 of the 5 bolts. I could pull the headliner down a couple inches and see it drip and get my finger on it. I put silicone on my finger and smeared that all over the bolts that were wet, but I couldn't get silicone all the way around them.
My thinking was "Well, if THESE are dripping, I know the other 21 in the roof are dripping too. Best to fix these damn things NOW and hopefully finally solve this water thing."
So I dropped the headliner, drove it around a bit, let it sit in the pouring rain outside, then drove it to home depot and back at varying speeds, pulled it back in the garage in the pouring rain, and...
not a single damn one of them were leaking or dripping. All but one of those rubber-coated jack-nuts were drawn up tight and 100% splayed out nicely (one of them can still be pulled up a bit more, which I'll do now that I can actually get to the other side of it .) That rubber watertight seal seems to have worked pretty damn well on those things. I'm really surprised. After dropping the headliner so easily now, I will now tell everyone to do the same when they want to replace the roof rack bolts. Just drop it...if you drop the headliner (15 minute job tops) you could hold these jacknuts from the inside and have a friend tighten the bolts from the top in an hour flat. Not taking the headliner down, it took me about 12 hours total to get all 24 jacknuts installed. It would be 1000% easier and faster, no contest.
So, I'll still coat all the bolts with some sort of silicone or spray rubber undercoating for insurance since I'm in there already. I see that jeep has a channel covering all of these bolts though, so I may have to either cut a hole around each bolt or get a hole saw blade and make them nice and clean with a nice 2" hole around all of them. Might weaken the roof a bit, but shouldn't hurt it much as I'm only taking a bit of the channel out.
I also got some permatex RTV hi-temp (650 degrees) red gasket maker to run a bead around the hole in the floor before I weld the sheet metal over it to try and keep water out, and then try and do something underneath it without R&R'ing the damn muffler. Maybe use some more spray rubber undercoating on it from underneath?
I also got some window gasket sealer, so now I need to R&R those two rear windows. There is definitely water coming in from the one on the passenger side, as I just saw water actively running down the inside of the rear quarter panel. Has to be coming from the window rubber.
I felt inside the roof channels with my fingers (the channels that cover the new roof rack bolts) in varying places and did not feel any water coming in and running down the length of the roof to the rear.
Little by little....