Performance problems

I recently installed my off road Mac H-pipe, and had a shop weld the middle together after I installed it. The first problem is I don't think the pipes were pushed together enough cause the driver side sometimes rubs against part of the undercarriage and is somewhat annoying. My check engine light now comes on once in awhile during acceleration. And the most annoying thing is the car still misses right after 4K when it is warmed up and your getting on it hard. I already gave the car a complete tune up in an attempt to fix this. Any suggestions to these annoyances?

Todat I installed a new ignition module, coil, and reset the timing to 14*. The car runs like a champ! I also installed a water temperature guage, cause the stock one doesn't work anymore. It stays steady at right above 180*. My only problem right now is to try to adjust the H pipe from hitting that bracket on the frame rail. I'm not sure sure what the problem was with the missing but one of these fixed it. I probably should have done one thing at a time. The loose hatch gets fixed today!