I should follow this up with some details to save the next guy some time and aggravation.
The bolts that hold the header on are M8x1.25. Since the bolt extractor didn't work, even with heat, I stepped up drill bit sizes until 9/32", where I was able to remove the remaining bolt material. (8mm = 5/16, but this would damage any existing threads, and I didn't want to do that). I was able to tap the hole and it wasn't bad.
I got some stainless steel bolts (stainless all-thread isn't the easiest to find, but the local Sears Hardware has a good selection of stainless hardware), cut off the heads, and ran a dye down the threads to make sure they were clean. Apply a little Lock-Tite to the base threads that screw into the head, tighten down, and install header using stainless nuts and washers.
Everything buttoned up nicely. I slapped in a new donut gasket for good measure. No leaks, no fuss, had a great ride testing it for issues.
One other note, while I had the exhaust apart, I figured it would be a good time to punch a 3/8" hole through the Dyna baffle. It sounds so much better.