Magellan, sorry to hear about all the pain your having with the system. I also had issues at first with my plastic cover, but never had any issues with the front clearance. I believe that the gasket problem has been a pain for everyone that has the system, it really does,for lack of better words, SUCK. But the sound and performance of the muzzy is EXCELLENT!
My best advice in fixing your clearance problem of the plastic cover is as follows:
Once the system has been fully installed make sure the muffler brackets are fairly loose, and go in through the cockpit (driver side) and loosen the header bolts just enough to have some play without the gaskets coming out of place. Then grab hold of the header just down stream of the plastic cover heat shield and and work the system upward. It will take some force, but I assure you from my experience there will be no damage done. The correct position of the head pipe should be out and above the plastic cover.
I have about 2" space between the shield and plastic cover and have rode as hard and as long as possible in the Arizona heat, and have had no melting problems. I dont even have any heat wrap on. I have removed the stock shield that you were having problems with and have not even used the muzzy mtr mount shield yet. Absolutely no heat problems in the cockpit at all. However I did have some factory wires beginning to melt, but that problem was easily eliminated by rerouting them.
Now your excessive heat problems sound like they might be caused by too lean of jetting. What jets are you running? I'm running the biggest jets from Todds kit and she's still kinda lean. Now the only problem that I face, but not really worried about, is my right muffler sticks out about 3/4" longer than my left one. I wont fix until I see that it's a performance issue. I have about 20hrs on the muzzys.
I hope some of this helps you out buddy....................
