Years ago, this was a huge problem that destroyed alot of cobra engines. Im afraid yours is probably gone as well. If you would have done a search on all the mustang boards, you would have seen MANY threads on the subject. People all ended up with scored cylinder walls, shot rings, broken ringlands, etc. It basically came down to this. Because of extremely poor quality control, the mac longtubes were filled with weld slag, weld remnants and all sorts of abrasive stuff...basically dirt or sand. You fire the motor up, and all the crap finds its way into your intake manifold through the EGR and eats your motor alive. I never did buy that excuse though, because most of the intakes have alot of oil built up in the lower plenum, which would catch most of this stuff. I believe the vacuum created in the headers during engine braking, as well as some of the resonant pulses were carrying this crap right into the cylinders. The flow isnt always in 1 direction. Anyway, I had the macs on mine, but mine were used and came off of a cobra that had already been eaten alive. It had been consuming so much oil that all the primaries were coated about 1/8" thick with carbon when I bought them. I hoped that because all that crap had already been blown out, that my engine wouldnt get shot. I flushed all the tubes with carb cleaner, hosed them out, blew them out with compressed air, and even took a die grinder to the primary entries. There was ALOT of weld sticks and junk in there when I started, but when I was done, they were ok. My engine never did get destroyed, but the quality did suck and they were prone to warping and creating exhaust leaks. i went through about 9 exhaust combos. By far the best combo was stock exhaust manifolds with a tightly sealed dr. gas x-pipe and a magnaflow catback. It sounded incredible and was faster that it was with the longtubes. Sorry to hear about your engine troubles.
Off topic: why do I have only 3 posts? I was one of the biggest posters on here.