Bitter-sweet update. What was left of the YJ was recovered:
A quick summary...a guy reported he saw a YJ with full-width D44/9" axles sitting at a shady mechanics shop. The owner and a friend immediately ran over to check it out, however it was not the same YJ (this one had a swapped in V-8, different trans and t-case), only the same type of axles. Considering rest of this YJ was pretty custom and the axle combo isn't that rare (last trailride this guy was on 2 other YJ's were there with these axles), and no way to easily check the gears and lockers, they left thinking that it was probably not the same stuff. However the local police snooped around this shop some more and found the remnants of the stolen YJ in the back as seen above, and the full-widths had been removed and replaced with stock YJ axles. Also notice how they quickly spray painted the remainder of the sheet metal, presumably so it wasn't as obvious to people looking for light blue. Based off that there is a good chance the YJ they looked at the day before actually had the axles from the stolen Jeep. Good thing is they have the plate # of the YJ in question.
I'm trying to get a list of missing parts so everybody can keep a look out for them.