So it's not quite as bad as I thought. I've mocked up the catback, removed the now-useless fuel-filler line, and pulled off an exhaust hangar that isn't needed with my catback (how did I miss that before?), and suddenly things are fitting a lot better. The taillights are off, and the bolts on the rear fascia are soaking in PB Blaster, so hopefully that will come off uneventfully this weekend, and I can see how much of the rear sheetmetal "wall" behind the bumper I can cut out to give the cell a bit more room back there. Regardless, I'm not going to be able to go quite as low with it as I'd hoped; after getting the exhaust mocked up, it's pretty obvious that the rear canister is in the way, so at best I'll be lining the top of the fuel cell up with the main floorpan of the trunk area. Not the most perfect arrangement (because I still need to put a bulkhead over it to be legal for tech, which will interfere with usable storage back there), but it'll have to do.
I think I have a pretty good idea of how I'm going to mount the fuel pumps now, and it's a bit different than originally planned. Instead of mounting them east/west under the rear seat area (where the stock tank used to be), I think I'm going to hang them from the fuel cell frame, one on each side. That simplifies the feed lines pretty dramatically, and the merging of the two pump outlets becomes pretty trivial too. That will start to come together visually once I start to get the frame welded in.