Afternoon All ~ I have a 09 R3T with 500 miles on it. When shifting it "Clunks" in pretty loud. Almost like an old Harley. Me being new to the Rocket family, I am not sure if this is normal. Clutch seem to be adjusted right.
They do clunk going into first. For shifting beyond that you may want to try pre-loading the shifter. It makes the action much smoother, not quite Japanese like, but close.
Yes, clunk they do ... mine still does after 16k. It's a little smoother than new, but not much. Those are some seriously BIG gears in there to handle the torque ... they do make noise. I typically don't use the clutch if I'm pulling on it hard, a slight burp on the throttle while "toeing" it works great for keeping the clutch from slipping under a load.
Have you had that first service yet? It'll get a little more smoother when they change out the semi-synthetic oil for the full synthetic oil. At 500 miles you are due for it, then not another "required" oil change till the 10,000 mile mark.