They pulled the wires off and put them back on. Must of had in the wrong order but I checked twice, oh well. Didn't run the compression test and still will but it is really cold in Wisconsin right now so I am going to wait for a warm day. Should I possibly just get another diagnositic on it also to see which cylinder may be misfiring?

The PCM will tell you which cylinder is misfiring. If the CEL comes back on, just go to your local parts store, and have them read the codes.