I don't like my 2010 shifts and went from HD to redline w/shock proof and now have Royal Purple in it. This is all within the first 4k just trying to get it to shift smoother. I really saw little difference in any of theml I had a 05 RK and though it had the clinck it could not have shifted any smoother. I would love to have that smooth "clunck" back and forget the quiet.
Wouldn't worry too much. 4k isn't much time for tranny parts to get friendly on the new boxes, especially if you have lots of highway time. It'll likely smooth out a lot by 10k. Might check to see that your clutch isn't dragging too much. That'll add some clunk too and its an easy fix.