Got both rear light covers swapped out and removed the intake manifold. I'm still not feeling so hot today, so I think that's all I'm going to do right now.
I was concerned about the difference in flange thickness between the new header and the factory intake manifold... it's about 1/16th of an inch, but I think that is why the rubber shims are there. I'll be taking the cutting wheel to the old exhaust tomorrow after a few more doses of Nyquil later today.
edit: Well, that didn't end well. I got the old manifold off and thought I had the rest of the exhaust secured. Nope. Now I have to spend money on new hangers. Also, the oil separator cover gasket I ordered was the wrong kind (I ordered the rubber one. It's a different size and shape than the original cork gasket).
Still don't feel well, so I'm going to put this off until next weekend.
$50 bucks for new exhaust hangers and a cork gasket.