i get the same noise on my bike... but sometimes i'll hit the sweet part on the RPM and i won't get any noise, it just goes in smooth as silk... but when i do that i'm not paying attention so alot of times it's by accident...

 

well sometimes when im accelerating hard and try to shift fast it feels like the shift is smoother and i dont hear the clunk. but i just assumed that i couldnt hear it due to the increased engine noise. i will give the clutchless shifting a go.

 

Don't forget to check to make sure the clutch cable is adjusted properly.
As stated, another potential problem is the drive chain being too tight.

 

I get it the majority of the time from 1 into 2 but not after that. i dont get it all the time though.

 

I know mine is an older bike , but I had a clunk. Changed to a different oil, and voila! clunk is gone. Don't know how well that would work in a newer bike, but maybe worth a try??

 

This is true, using a full synthetic will help your bike run and shift smother. Cost 4 times as much as well.
I use it though.