I appreciate everyone's input, and especially the older posts that I found when searching. I understand how that goes. I help run a rather large F-Body board and I know how it can be when some of the same questions pop up over and over.
I could talk someone through completely dissassembling and reassembling a late model Camaro or Firebird over the phone, but I haven't quite gotten to that point with my XJ yet. Hopefully soon.
Anyway, here's what I ended up doing so if someone ends up searching in the future...at least I've got my .02 in.
In hindsight to all of it, PB Blaster would have been a welcome addition to this project. I ended up using a combination of a hammer and a punch and an air chisel to knock the nuts/broken bolts out of the holes. From there I took a 3/16 x 6" drillbit and drilled up into the holes through the cargo floor. Where the bit came through I cut an "x" in the carpet and peeled the carpet back and used a hole saw to create an access to the back side of the holes. From there it was as simple as using some 5/16-18x1" GR8 bolts to tighten everything back up. Tomorrow I'll use some spray adhesive and glue the carpet back down, and it'll look just like new. (Ive done the same on the cage in my T/A, and you can't tell there's an "x" cut in the carpet.)
That's about it. Hopefully this helps someone out down the road. Now it'd be nice if I had to do something like this to repair damage from using this thing instead of just routine maintenance.