The studs and bolt I'm using for the turbo to downpipe connection are still intact at this point and came off fine. I could replace them while they are out, but should I bother?

That connection sees much less heat. If you want to save money, just reassemble with some anti-seize. Nissan Inconel hardware (I've got pix in my build thread) is pretty cheap though.

Now that I've asked, the downpipe connection will just completely fail on my first autox run after the car is put back together.