Ok... I installed the down pipe from Hogan performance. I can hear the difference! Sounds strong!
Well, for the cylinder #1 misfire it was still there. My coil went bad, the way I tested was swapping the 1&4 coil with 2&5 coil. I erased the code and started the car again, still had rough idle plugged in the reader and there it was cylinder #5 misfire. I wonder if the air leak caused a coil to go bad or just coincidence. I did drive it 19 miles home with a cracked flex pipe. These MSD coils are maybe a year old. However, I put my old Gm coil in and it is running fine now.