I replaced plugs and coils and valve cover gaskets?

My car was running fine right after I finished the coils, plugs, etc. I was sitting inside the car with it idling and noticed several weird things happening for one radio had message displayed on radio interface saying low battery and realized my car had cutoff it was raining that day and I scanned codes and it had an exhaust gases recirculation code and a code saying something about the evap pressure sensor. The car seems to have a short somewhere around the wiring harness that runs over the top of engine on passenger side. When the harness is moved the engine will smooth out and when I let harness go back to its original resting place car misses and sputters and can smell gas and see black fumes coming from tail pipe.