It sounds like excessive valve clearance to me, if it is a ticking or clattering sound rather than a knock or deep solid sound. The 99 and 2000 models had a cam chain tensioner recall. There were two recalls, the first modified tensioner did not work, so the second recall required an oil pressure cam tensioner to be installed. I have a 2000 and delayed getting it done until 17,000 miles, never did make any noise or anything but after reading some of the posts on what happens when the tensioner gives out (destroys motor) I got mine done. The dealers will do it for free... I don't know how you would go about it. I have not been active on the board much in the last year, but I seem to remember that you can raise the tank and see the fat oil line they installed for the 2nd generation tensioner. I would reccommend emailing Busa11K or Motorhead or one of the guys who are good mechanics and get some advise. Also, if it is making noise and the recall has not been done, don't ride it! Don't even start it! You can do a search and probably find lots of info on the cam chain tensioner. I have also heard that the oil actuated one can make a bit of noise just before it ratchets to the next level of tension, although I have almost 30,000 miles on mine and it never made any noise, before or after the new tensioner. The fuel filter and/or injector screen clogging problem was solved on the 2000 models, but you probably have the aluminum sub frame assembly, unless someone changed it. You can do a search on sub frames also. They have had cases of them cracking and causing crashes. Remove the front seat and check real good around the welds on the frame to subframe section . They broke on or near the welds. I put TTS frame braces on mine and check it regularly and have had no problems, even with over 100 pounds of luggage on long trips. It is not reccommended to install hard bags on it, especially Givi bags. Email me if you have a problem getting answers.... I don't check in here very often anymore.
Mike