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I switched to Amsoil Sever Gear 75w90, and really haven't noticed much of a difference in sound. Still clunksa little, and neutral is still easy to find. I switched from a Honda cruiser and there are all kinds of new noises I am still not used to yet. Valve train noised, pushrods, clicks, ticks, and taps. I still hear my engine even over the wind and my exhaust. Just the nature of these beasts.
I came from jap bikes to an 07 Fatboy, I noticed the clunk right away and wondered the same thing, I am not totally used to it but kind of like it now.
That's because compared to most of the metric and Euro bikes the tranny on a Hog is more like a semi's.
Its also a devorced system unlikemost other bikes who have the tranny inside a wet sumpcrank case.
I think alot of the clunk sound is the slack in the primary chain that connects the tranny to the engine. It is normal adjustment to leave slack in the chain. Anyway it is normal. I think harley leaves things like the clunk in there to keep the nastalgia part of the experience alive. If things were smooth as silk it just wouldnt be a harley. Gotta love it!!