Hi Simon,
I recently installed a new 389 which also came with the "correct" jetting set up.
After installing it the bike was very reluctant to fire, and just when I was about to give up, it finally fired, but was running very irregular, and I couldn't get a decent idle
I went out and got myself 2 pilot jets, one a size bigger and one a size smaller, and after some experimenting, the smaller size went best, and is still in doing a perfect job.
I also needed to experiment a bit with the needle height, because at 1/2 to full throttle it was running to lean. I ended up with the needle in 5th from top. I didn't like it to much that way, so I was about to change main jet to a bigger one, but I found that gradually things where improving, as last time when I inspected the plugs, they where a bit sooty so I dropped the needle a notch. Took it for a long drive this afternoon, and it's behaving perfectly now.
It seems that a new carb needs some "running in". Mine certainly does, because it gets better with every mile I'm doing!