In the grand scheme, a little oxidation on the header pipes is the least of your worries in terms of keeping your bike properly maintained and running. I had a similar quandary, when restoring my 750 (check link in my signature for thread), and in the end I had the pipes "ceramic coated", which I somewhat regret. Hot Jet is similar to "ceramic coating", but in truth, it's just a high temp powder coat. The gloss isn't great, but it can be polished to a higher sheen. The problem with my pipes is that the finish is somewhat fragile; there is a chip on a header pipe of my bike with a chunk of the coating came off, and now I'm afraid to touch the rest of the system, for fear of more chips.
The problem with chroming used exhaust systems is concern over contamination of the plating baths. Most places won't touch a motorcycle exhaust, for any price.
Oh, and BTW, I think you nailed the reason for the deteriorated chrome; the air injection system. Even if you get new chrome, it will suffer the same fate.
Good luck with your project, and welcome to KZR!!!
