I bought a fuel pressure gauge today and I found out that when I was getting those power losses, my fuel pressure was dropping drastically. Turns out my high pressure fuel pump is bad - and it was new. It was either a bad one or I had it in too hot an area. In either case, I'm going to move the next one to a cooler location. Not sure why my plugs were dark. The engine seemed to run better with the mass air.
Anyway, thanks for all your help TurboCoupe50, much appreciated.
Scratch that. I found out that it's purely a vapor lock problem. I've moved my lines and my pumps and the problem isn't nearly as bad, but it's still there when I sit in traffic for a little while. I might try wrapping the metal lines going into the engine with some heat wrap. They seem to be in the hottest spot of any of the fuel line.
Thanks again TurboCoupe50.