Clunky Gearbox?

On my bike the worst clunk is from second to third gear, even worse then the change from first to second, is there a reason for this? makes me cringe everytime, does anyone else notice this with there bike? any technical experts out there as to why this, second to third gear should be so bad? the rest going up the box isnt so bad after . love the bike, but almost convinced myself, there must be something wrong with the gearbox to be so bad, even though ive had lots of reassurence on here
 
I have an 06 classic and the clunk got louder after the upgrade kit which second gear on the new gear has less pawl's on the gear to help it go in easier. My only complant is when you shift at 7000 it tends to pop the front end up for some reason except from 4 to 5th but then that is over 130 when I shift into 5th. I thrash mine so if yours is a newer one you should be fine. Besides after the grin factor happens so much your smile will force your ears closed
 
Hi pedro, ive also got that strange high pitched whine as well, married her 8 years ago, and it gets louder every year
 

Gotta agree completely. Rode her today...clunking and all...had a repellent yuppie in a BMW x5 (I think...the SUV iteration anyway) cut me off on the highway accelerating and I just had to spank him a bit by blasting past the clueless lad. VERY satisfying to B-Slap this fool with the beast! So fun!
 
If you ever have the oportunity to look down into the internals of a Rocket, you will understand the clunk....it looks more like the inside of a Peterbuilt.

Maybe coincidental but my "whining" went away after installing the K&N's