I would look into your water pump shaft seal if you haven't addressed it yet. Mine was loosing coolant with no leaks and it ended up that the seal had failed. Common issue check go to http://www.ktm950.info/
section step by step instructions on replacement. I used the Cjdesigns kit. Good luck.
2007 KTM 950 Super Enduro R: titanium Q's, CJ Rack, H2W Jetting, Scott's triples and dampner and more to come.
2005 CR 500AFC: Need more be said BEAST!!!