Yeah mac products suck! I've had plenty of them in the past. I had the same problem with my foxbody, and mac wouldn't do a damn thing! I sent multiply pictures and they claimed that my installer didn't know what he was doing. BTW he is a fabricator, does many chassis work, cages,mini tubs, full tubs,ect. We had to end up cutting the midpipe and he added bends to make it work. I'll never buy there products again and I told them that. They didn't seem to care.
There are lots of people running Mac products on their cobra with no problems including the prochamber. I wish they still made a catted shorty prochamber. I have mac long tubes that fit like a glove and no ground clearance problems.
Wait for others to chime in. Do you have any photos you can post of how they're being installed and where they're hitting?