I had a similar issue; with the HD poly bushings, they just put the bars up a little higher and the rubber trim pieces on the inner fairing didn't match up to the bars. The poly compresses slowly, I retorqued the risers a few times, waiting several minutes in between so the poly would settle. It helped to draw them down a lot but I still ended up disassembling and milling an 1/8" off the bottom of the risers. Dont know if it will work with the RK but its a clean fix for the Glide. I would think the 1 1/4" clamps might need a little more taken off the bottom.
When you say handlebar cover do you mean top clamp piece or fairing cap?
talking about the cover that the post below yours showed a picture of. When I had my RK, I went to the fat RK bars, HDs required parts list showed the new cover as being required. When they put it back together on mine it wasn't needed so they refunded me for the part.