Yes from what I see this is a very common problem on these bikes, my cvosg did the same thing and I also dropped a line on this forum, bleed the clutch which made things work better could actualy find N on about 3 tries, Then with feedback from the great minds on this forum I was convinced into changing the trans fluid to Spectro vtwin trans 75-140 and let me tell you,
what a difference, much easier shifting and a lot quieter. (since then I also changed the crankcase to Royal Purple syn 20-50 another big improvment)
You will find that as you put some miles on your new bike most of the rattles and clunks etc seem to work themselves out, I have 900 miles now and every time I ride, it seems more enjoyable. Maybe the MoCo should break these in for us! it would settle a few nerves...
Oh ya, I had to have my battery changed under warr already, so don't be surprised!