Using 0000 steel wool and Simichrome, I was able to clean one side of the headers as an example. Here's the before (passenger) side: (I hope the images resize to something smaller)

before cleaning.jpg

Here's the after (driver) side:

after cleaning.jpg

I think that it's worth removing the headers, or at one bolt at a time, so I can detail this a little more, not just the headers, but the engine, too. There are still black spots where the rust was, but there is a marked improvement. Thanks to DA43GUY for the advice.