I tried to look it up but didn't really find what I was looking for, so I thought I'd pose the question.

I have a 99 XJ with too much rust to fix so I'm looking for something broke down with a rust free body that I can swap everything in to.

The problem that I am facing is the lack of 97+ Jeeps in my area. There are a few older bodies though. If I were to go that route, does anyone know what would be a direct fit and what wouldn't? Axles, TC, engine, etc... (Also, whether the steel hatch can be swapped on?

My engine and tranny are in good condition so everything could just be swapped, but I just don't know how much fab would be involved in that, if any at all.

Not much. Biggest problem would be the electronics to run the engine and transmission. There is a sticky at the top of the forum about engine interchangeability.