Welcome to the Forum! I am also a Chevy guy, see my avatar for a pic of my stable including my '74 Corvette resto-mod, which I still have along with my '68 GTO which I just picked up in Feb.
As a relatively new guy I can't answer all your questions, but I'll take a stab. I'm sure one of the more experienced guys will jump in shortly.
1. Rust around the back window and rear window panel is common, as always check rear quarters and lower front fenders behind the wheel opening. If it has/had a vinyl top check underneath, around the window trim, and at the lower trim at the top of the quarter. If any of these are rusty or leaking check the floor pans. Lot's of repair sheetmetal available but as you can guess you can easily spend more than the value of the car fixing rust if you get in too deep.
2. rear taillights/bumper, front signals and side markers, slight grill differences, I think the hood scoops may be a little different but not sure. Some small differences in the dash I think. I wanted a '68 in particular so I didn't study the '69s much.
3. I'm sure this is possible, not sure if it's worth the effort, although judging from your next question I think I see where you're going with this question. (Judge Clone)
4. The Judge was not made in '68.
Best of luck, but I would be careful about buying a $2K muscle car, could be a real steal but could also be a real dog that someone is just trying to unload.
'68 GTO, 400/TH400, AC/PS/PB/PW/tilt, hideaways, Hurst dual gate
'72 442 'Vert, 350/TH350, AC/PS/PB/PW/tilt
'71 Javelin, 401/4-speed restomod
'74 Corvette, 383/4-speed, 450 hp, restomod *SOLD*
'70 Cougar XR7 'Vert, 351W/FMX auto *SOLD*