If your bike is running and in neutral, pull in your clutch lever, blip the throttle a few times, release the clutch, pull it back in and then shift down to 1st gear. This should help the clunking. This does not indicate a problem with the bike, I had a Kawasaki KLR650 and you HAD to follow this ritual when the engine was cold, otherwise the bike would not only clunk, it would actually jerk forward and stall the bike, causing a stream of bad words to fly from my mouth and much humiliation if anyone was watching. This was a common issue with the KLR's. As far as your 1st to 2nd shift, be firm and quick on the shift. This will improve as you break in the bike.