My 2006 Fe450e had rear tire rub. Dan gave me a new tire but I had allready shimmed out my muffler. I bought longer bolts and 1/2 thick nylon washers at my local home depot. The muffler can shimmed out real easy. It put no stress on the pipe. I had to roll back the outside fender support tab. I'm glad I shimmed it out so far, 5/8' in back and 1/2' in front becasue I think that other tire Dan gave would have still rubbed.
My theory on the 2006 models is they made the tank narrow, so they had to make the Hips narrow too, and the muffler set up is too in on the tire.
problem fixed. Bike is awesome.