Mileage will help..
I now have 8200 miles on my 05' and it is getting quieter with regard to the "clunk" which I thought was awful in the beginning until I road with a couple of guys with brand X bikes that were even worse.
I also changed oils to Mobil 1 Synthetic and noticed two other things. One, was the running temperature in the oil reservoir tank went down about 10 degrees, Two, the clunk either lessened or I am getting more used to it.
I have also been giving the shifter/seal area a little squirt of Zep 45 on occasion and found that the shifter seems to exhibit a lot less tension and is much smoother upon activation with my foot. You might want to try this too.
Be patient..it will improve with use...SB...