idling trouble

ok well first off i own a 1997 honda civic hx , ive done quite a bit of mods too it and found some trouble. My car ran really good for about a month or 2 with all the mods i have done to it

aem cold air intake
dc sports 2 piece header
tanabe catback
msd sci ignition blaster ss coil nology wires
apexi vtec controller

so the other day i raced some jerk in a civic that thought his car was fast on the highway i get off the highway goto my friends house after all this and my exhaust was like poping, it sounds as if at an idle its missing a cylinder my friends an a few mechanics i talked to said that the ignition was the problem to prove them wrong i took the ignition totally back to stock along with putting the catylitic converter and stock exhaust manifold back on. the controller reads normal i havent touched it since the car was dynoed. i also checked if the timing belt jumped or anything nothing. i was wondering if there was ne mechanics out there to help me out ?

new plugs , rotor, cap , fuel filter