The wiring/lighting issue mist be traced using a diagram or pulling and following. I suspect your flasher/braking circuits are shorted or crossed or grounded through the flasher. As for the rattle fron the exhaust, if the heat shield screws are tight, I suspect the tack-welded screen in the muffler is loose.
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2009 XR650L Big Red Pig
Tusk bar risers
2007 X-Moto(Jetmoto) GY250
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15/40 sprockets
UNI Pod Filter
2007 Shineray TMS 200XYi--Betsy 
Betsy Mods:______________________
Acerbis DHH headlight
FMF Powercore pipe
Uni Pod Filter
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