I'd be very careful messing with those studs. I am not suggesting you do nothing. Indeed, I am suggesting you take great care and NOT do nothing. My recommendation is to spend some time (days) squirting penetrant on the nuts and related areas. My favorite is Maltby's. John Walker likes it too. It looks like this:
At their website, they want $75 for a can, which is ridiculous.
maltbystore.com
Insanely ridiculous. You can surely find it much cheaper. I have found it at places where mechanics work on diesel stuff. It really is the best, but just hard to find.
After a good soaking, I would then HEAT the nut. This will cause it to expand and become easier to remove. Oxy/acetylene is the kind of heat to use. Or MAPP. Get the nut cherry red, then remove it.
Once the nuts are off, and the old exhaust, then I would go after those threads with a wire brush until they are shiny. Not sure I would do much more than that but if you want to carefully chase the threads with the proper thread-chasing style of die, then go ahead but be careful. If you break a stud, then you will be drilling it out. You will be drilling a hard steel stud out of soft aluminum.
Penetrant > Heat > Removal while cherry red > wire brush the threads