Good thought to check clearances; I saw that the 950 folks were worried about an extra inch higher on the low guard too. Sorry if I am missing some nuance to your post; it sounds like you are hoping that there is more room to raise the stock low-boy than the published specs and your measuring afford...
KTM website lists what you have already figured out:
Suspension travel front/rear 275 / 300 mm (10.83 x 11.81")
So you are thinking you have less than a half inch of additional clearance (6/16th) - probably not enough considering the other fun? (longer crossover brake line?) I know you will have fun making the Al tabs to raise the bugger!