I had to do the same kinda thing with my 929RR and the Scotts damper. I was able to get it where it didn't put any stress on the damper though. Dunno if that's possible with the 1000RR.
Soon after, I switched to the lower-triple-clamp method of tie-down. You just have to get the angle of the tie-down points right so that you don't put any stress on the inner fairing. Depending on the truck/trailer layout, that isn't possible in all cases.