Motorcycle Repair: Yamaha exhaust, lean mixture, exhaust pipes

Question
Hi,
I am new to motorcycling and recently bought an '02 650 V-Star.  One of the exhaust pipes had a brown dicoloration about halfway between the header and the end of the pipe.  I removed the pipes and cleaned them but they don't seem to fit back into mounting position very well.
1) Regarding the discoloration, what may have caused it and how can I prevent it from returning? (A coworker mentioned a lean mixture and carb rejetting.)
2) Is there a problem with removing the exhaust pipes for cleaning that would lead to a remounting problem? (The one pipe now interferes with the operation of the rear brake pedal.)

Thanks for any info.


Answer
I usually only answer questions on harleys, but I think I can help. You pipes discolor from the bike running lean. They come from the factory lean to pass EPA standards. Get the carb rejeted and that will help with the problem.
As to remounting the pipes. Loosen all the bolts holding the pipes in place and move the pipe around to where it belongs and then retighten and that should help.
Good luck and happy riding
Mike