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Cyl 1 Random Misfire 2006 GT, Whipple Supercharged


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Ok... let see what you all think of this:
My 2006 GT with Intercooled Whipple has been going into limp mode for some time now. It pops a 300 (random misfire) and 301 (misfire Cyl 1) each time. I replaced the spark plugs with Ford Racing plugs (same as ones that came in Whipple kit). Also replaced the coils with brand new Accel coils. No bueno! So I swapped the number 1 and 2 fuel injectors to see if the misfire would jump to cyl 2 and it didn't. The local performance shop looked at it and pulled the injector plugs and cranked it over to see if it sounded like it was losing compression and it sounded fine. I also changed the mass air sensor even though I was pretty sure that was not the problem. It seems to kinda surge sometime when I accelerate. But most times it drives just fine whether im flooring it or just cruising.

Any ideas???