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.