5.0swat

I owne a 94 mustang gt 5.0, i had to replace my transmission, so i swapped out the automatic trani for a t5 5 speed. the car is running strong, accept for some reason it is missing, or hesitating bad periodicly. there is no flux in the rpm gauge, so i dont think the clutch is slipping, it kind of feels like its not getting gas for a split sec, and looses power, but then kicks back in. It doesnt do it all the time, but every so often, and only when there is a steady preasure on the gas. i have put a new fuel filter on it. about 2 weeks before i changed it out, i put a cold air induction system on it, but it wasnt doing this until i chaged out the trani. can you please help! its driving me nuts! thanks jwhite