Clunky gear shifting ?

I'm just going to speculate about that sound, I have an 05 r3 so I know they do have a agricultural sound when shifting; maybe you can try changing the oil and the final drive gear oil, "Remember I am just speculating, good luck and be safe"
 
I'm late to this party, but every bike I've ever fiddled with the transmission will get clunky when its good and hot. Mainly after say 100 miles in my experience...I just think it's the nature of the beast in bikes whose transmissions have to bathe in the same oil that has just been cooking in the engine. No long term harm, but the parts expanding from heat cause odd fitments, and strange shifting. It all sorts itself out when the bike cools down.
 
I thought my bike was quite smooth in the gearbox dept.
Got it back the other day after having the detent spring done and I **** you not it's even smoother ????
What is involved time & $ to install detent spring.
My 2008 classic slips our of 1st sometimes when starting and slips out of 2nd on the way down.