cold start really ruff..?

Hey guys looking for some answers. Got a 07 GT 5speed with a Saleencharger. Kooks long tubes with catted x pipe. Running the Saleen Upgrade cold air kit. Anyways the car has a JDM Engineering email tune. Lately the very first time I start the car in the morning it starts real ruff. I tried cleaning the throttle body and so on and no diff. Once the car is warm it starts with no problem and idles great. Some times it seems to idle a little ruff also?? All the vac lines are good and its not throwing any codes. About a month ago it threw a slow 02 code but i cleared it and nothin since. Im thinking maybe the plugs are starting to go. Im running the HT0 gapped and 32 thousandths. I put a oil seperator on due to some oil in the throttle body havent changes the plugs since then, could that have something to do with it. Anyone have any ideas?
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Sparta thanks ill contact JDM and see what they can do, lastnight i put my old tune back in and started the car this morning after it sat all night. Still the same thing, cranking for about thirty seconds then starts and runs ruff for like 30 seconds and then clears up.. Kinda makes me feel its something else other than the tune because it never did it untill like a month after i did the longtubes?.. I'll check with JDM and see what they have to say though.