Clunky first gear.

[Ward P]

are you putting it into first with the choke on?

Gen2's don't have a choke (fast idle), well mine doesn't anyway.
Mine has 400k's on the clock and does the same, although only when it's dead cold and only the once. I was a bit concerned too, but Camel has now put my mind at ease (thanks mate ). My old gen1 sounded like the gearbox was going to fall out when I put it into first .. cold or hot

All of my previous bikes have done this. My 'busa ('99) never has, always a soft little click, no jolt, even from cold after a long rest. Heard it's common on the Gen2, but not so on the gen1.

If I don't hold the brake on, on my old honda when I first engage 1st for 1st time from cold, it near launches across the garage with a huge "Ker-lunk" after that it's smooth as silk. Never worried about it, it's just one of those things bikes do. Just be firm and precise with that first change and it should be right from then on.