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.
2015 KTM 690 Enduro R, 2007 KTM 990 SuperDuperEnduroR Sale Pending, 2014 KTM 250 XC-W