[steve00s]

First of all welcome to the forum. Did you get a CEL through all of this and if so have you been able to read the codes? That would help diagnose. If parameters get totally out of whack the car will go into "limp home mode" by shutting down a cylinder (disables one of the injectors I believe). This will cause the car to miss badly but should still run. Sounds like there is something more going on here. Headers and the O2 sensors could be a culprit but the codes will shed more light.