check engine light on and off

Recently I took out my stock air box and put a K&N Filter on when i went to get my car inspected it failed do to a hole in my down pipe. So I bought a 3sx performance downpipe (performance peice $300 cheaper than the stock peice).

My check engine light has recently started going on but it only turns on when im idiling. If im giving it a little gas the check engine light turns off. Has this happened to anyone and if so what did you do to fix it.

Also has anyone with a 91 done the one wire snake eyes trick. Since i've done it my sport and tour lights blink once in a while.

Thanks

judging just on this statement "Recently I took out my stock air box and put a K&N Filter on when i went to get my car inspected it failed do to a hole in my down pipe. So I bought a 3sx performance downpipe " your check engine light is on because your o2 sensor or your mass air flow sensor. check the connections. when u took out your stock airbox did the honey comb in your MAS look damaged? it has to be one of the 2...unless the snake eyes mod really messed with your electrical system