Try OTR?
http://www.off-the-road.de/en/XT-660R-X/Exhausts/OTR-Racing-Headpipe-XT-660.html
About the same price as genuine parts at �180 for the pair, although they're bigger bore and made out of decent stainless that will stay shiny (unlike OE headers). However, if only one's is dented the Yamaha headers can be bought individually.
I believe CRD make some too and are sold through X-Racing?