so I take it you loosened the lower triple clamp as well which you didnt have to do to remove the clipon. all you had to do is remove the upper triple clamp. place a jack under the motor with a board on top of it and jack it up and tighten the triples.
if you didnt loosen the lower triple the forks should have stayed where they were set. so your lower triple pinch bolts may have been loose. jack the bike up to the proper level and make sure the pinch bolts are tight and you should be good to go. I stated pretty much the same thing in your PM