Rattle when shifting into 2nd gear

Have you fiddled at all with your clutch adjustment? Sounds like its clutch related.

I have been thinking it could be the clutch too. Have you checked to see if the plates have worn the basket, this can make the clutch bind a tad as you pull it in but if left for a bit (even just long enough to let the revs die back a bit) can cause the shifting to be a bit clunky.

I agree its probably related to the clutch. I will start by checking the adjustment and see what happens. The clutch is one of the few things I did not take apart on this bike. I could see the friction plates were in good shape. I may have to have a look at it though.