I'd simply find another shop for alignment. Rear frame rust has exactly ZERO to do with front end alignment unless they want to do a four-wheel alignment, and unless the frame rust is causing suspension parts to move or come OFF.
BJ, CV's, hubs, those are all-in-one-day jobs. BTW, how do you "adjust" hubs???
Your issues are all simple maintenance items aside from the rust. Do each thing one at a time and it will be fine IMHO. Get some rust-converting spray, pressure wash the rusty areas and treat them with the spray, then paint over them with Rustoleum. I think you could let it be for the time being until you can get the holes fixed. They're obviously not going to affect anything but looks at this point.