I put a jc whitney baffled exhaust pipe on my Dad's 05 s40. With just installing the pipe, removing the air fuel mixture plug, and adjusting the mixture as per the instructions found here the new pipe blued alot at the point on the pipe where the baffle starts inside and to where the new pipe connected to the old header.
Is that a bad sign?
I didn't do anything else to the carb either. I have a jet kit I can use but the bike ran fine without doing anything after installing the pipe. Revved fine with no hesitation all the way through from zero to full rev. My Dad says it seems smoother when he test rode it and performance definately hasn't decreased.
I also can't seem to get a good seal no matter how hard I tried moving the adapter around that came with the new pipe. There is a leak in that area that causes some popping but my Dad likes it. Everything else was great. Real easy install.

I'm not sure this works or not,but I heard if you wrap about 18" of thick copper wire around the header as close as you can to the head,it will stop the pipe from bluing,if you polish the wire first it looks kinda retro, I would have done it to my bike but the pipe was blue when I got it,it only supossed to work on new pipe ????????

I made the mistake of NOT cleaning my supertrapp good enough and it blued on me. IF the bike is still running good and there isn't any air leaks then that is probably what happened (not cleaned enough).