Got it all back together and passed emissions. I ended up replacing the rear cat on Bank 1 with a Walker 140 dollar special and installing a no-weld Glowshift O2 sensor relocated on the pipe after the cat to move the rear sensor backwards behind the new cat. I extended the wires on the rear sensor and put on a longer fiberglass heat tubing to insulate it all. No broken studs either, I soaked everything with CRC's Knock er Loose spray and let it soak for an hour and then slowly worked the nuts back and forth until they came out smoothly. That stuff works better than I expected so I'll be keeping that in my toolbox going forward.
No leaks so far, I used plenty of copper exhaust gasket maker in addition to the normal gaskets, that stuff works pretty well. In the primary cat I saw a spiral metal thing that I think used to hold the cat so I cut that out and removed but that was the only surprise. The muffler piping is rusted together pretty well so I couldn't get that out but that will be next up on the list along with a compression test, but I have a feeling that the cats been missing for a while now so I might be in the clear.
Sidenote, I didn't end up needing to use it but I found that if you split the sensor wire from the bank that has a working cat and connected it to the truck side harness for the non-working side (so one sensor is sending signal to both inputs), the X accepts the signal and passes the emissions self test that goes on.