To answer a few questions, my symptoms have been observed in Cobb's OTS maps stage 2 87, and 91. I run 92 octane here in Oregon with a 10% ethanol blend. I have 45k miles.
Some more background: I have 2 levels of symptoms; stutter and rough acceleration under load, and secondly a flashing CEL as a result of misfire. I have thrown a flashing CEL 6 times over 5 thousand miles, all of those have been on cobb stage 2 (after I installed my Cobb FMIC). When the code gets thrown the idle goes very rough. I slow down, let idle and turn off engine. Upon restart it is fine again. Each time the code was P0301 (cylinder 1 misfire). The misfire code has happened 3 times before I changed plugs, and 3 times after. Each time the CEL has thrown has been under WOT on a rainy moist day. haven't had a dry day CEL, but the rough acceleration can still be felt (its not as bad on drier days though it seems).
As far as my troubleshooting thus far
1: I had a CAI installed, I took it off. One less thing in the mix too worry about.
2: replaced stock plugs with SP-542 plugs spaced at .028
3: Removed plugs and spaced them to .026
4:I reached out to Goose Tunes who regularly tweaks with the Cobb platform. I sent data logs and has been very helpful and responsive. I tried out a map he sent me and my issue was still apparent, however not as bad (kind of an in-between of stage 1 and stage 2 OTS I thought).
I was thinking of swapping coils around, but since I can't consistently throw a CEL deliberately I was planning on just replacing the coil pack on cylinder 1, and re-inspecting my spark plugs for insulator damage as my next course of action.
I have also observed my symptoms to be similar to condensation build-up in the intercooler. I don't believe the cobb intercooler has a drain on it like some other aftermarket intercoolers. Not sure what to think there.
I'll also reach out to Cobb, any Cobb raptor reps on here before I cold call them?