My 08 CVO Ultra, clunks too, but it is inherent in these bikes. I have 500 miles on my bike, and I'll wait till 1000 and drop the SYN3 then and go with Amsoil or the Mobil V-Twin. The tranny needs a higher viscosity oil than SYN3.
I also have a slight whine in first gear. Was told it was normal because it is a helical gear. 
DOG
Straight cut gears (spur gears) are actually the noisier of the two types, the helical gears are quieter. First and 5th in the Cruise Drive trans are spur gears, and thus noisier than 2, 3, 4, and 6 which are helical gears.
As for the "clunk" when shifting, that is caused by the method used to engage the various gears. In the older transmissions the actual gears would slide side to side to engage and disengage dogs & slots in the sides of the gears. The Cruise Drive uses separate shifter rings, but the principle is basically the same. The amount of free play or "slop" in the fit of the dogs to the slots is larger in the lower gears, and smaller in the higher gears. Therefore, more "clunk" and more on-off jerkiness in the lower gears versus the higher gears. This is done this way because there is a larger speed difference between the two gears in the lower ratios, and a tight dog to slot fit would result in many more "missed" shifts when the dogs bounce off rather than drop into the slots (the two gears are turning at different speeds until the dogs lock them together).
One thing that exacerbates the clunk issue, especially when engaging 1st gear from neutral, is a dragging clutch. Try this trick if you tend to get a loud clunk shifting into 1st: Pull the clutch in, rev the engine with a quick blip of the throttle (to break the clutch plates loose), let the engine return to idle and count to 5, then move the shifter into first. When done properly, you won't get any clunk or jerk. This is because the two gears have had time to slow down and there is no longer a large difference in speed between them when the dogs engage the slots.
Jerry