I'm going to raise my lowered 2011 TE 630 using its stock suspension link, and since the forks are also sticking out from the top triple clamp by a fair bit, I'm guessing the front end was lowered also. I would guess that the forks should be clamped in place so that only the removable cap is visible, but I can't find anyplace to confirm that. Opinions?
Position in the triple clamps is usually a matter of personal preference, given that it changes ride height, with a bit of performance/ handling concern as it slightly adjusts the rake angle of the forks. I leave about 1mm gap between the bottom of the cap and the top of the clamp. Use calipers or another fine, accurate measuring tool and make sure they're equal.