I have recently installed the headers from Fuel Moto and CFR exhaust. Right were the clamp attaches to the exhaust pipe and header the exhaust is turning brown. What could be the cause of this? Is there any way to get the brown/burnt look off the exhaust.

 

What year and model?
Are you running a tuner?
If you can post up a picture that would help also....

 

I'd say it's either from not cleaning the pipe thoroughly after installing, or bike's still running too hot. Venture to say it's the latter & you can check by pulling/looking @ plugs. If they're white - too hot & need to tune...

 

Like everyone else said, first guess is that you are running too lean.

 

Since it is turning brown/burnt where the muffler and header connect to each other I would suspect it's an exhaust leak. Normally pipes affected by a lean condition will turn blue or gold. I always une Pentox HI Temp RV on the inside of the connection end of my muffler before installing on the header pipe.