I had an issue like this and it ended up being the harnesses from two of the coil packs were switched. It would have a hell of a time firing and make all kinds of popping noises when we tried starting it. Have you tried playing with your spark settings? Try and set it up for waste spark and see if that helps. Mine is now set up for direct fire but when we were first doing the initial tuning it would start and run better in waste spark configuration.
Also what coils are you using? I have EJ25D heads myself and I found that the WRX coil packs and plugs were the correct length for those heads. I initially had STI coils but they were too short and the spark had to arc an extra gap. See this thread.
I LOVE your car by the way! I saw it at WCSS and I was really impressed. You should post a picture of it here, maybe it would motivate people to help you more