Unknown Problem

I not sure if this is a engine issue or elctrical, but need help to narrow down what it is. Heres the deal, my car sounds like it as a miss. I was messing with the exhaust last night and when it makes the miss noise, the exhaust flow is harder than the normal idel flow. It is also not consitant, sometimes it is every once and a while or sometimes a couple times in a row.
Any thoughts?

Thanks