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So after 6 agonizing hours, I removed my (M88) headers to get ceramic coated.

While I'm waiting for the headers to get coated, I was going to:
1) Chase all the threads in the head and clean them up perfectly
2) Remove the factory steel studs (about 1/2 came out when I removed the headers) and replace with new stainless studs
3) Install copper M6-9mm nuts

Thoughts?

It really depends on what grade studs you can find. Standard Stainless Steel fasteners are usually about a Grade 5. Stainless also galls very easily and you can have a problem installing and especially removing them. I would just use the standard studs and copper locking nuts. Unless you have a thread in the head that is messed up I would also not chase them with a tap as you will probably just loosen up the fit.

Really great advice.
Thanks!
I appreciate it.