Welcome, cool bike. Just so you know, 1999-2001 had a transmission upgrade to repair 3rd gear problems. You can no longer order parts for the trans. You may be able to find NOS parts for it, but most people havenít had any luck that way.
Most people swap in a 2003-2005 motor. Thereís a few threads around about the swap.
Personally if it were me, Iíd tear it apart and see if you couldnít grind the dogs on the affected gears if thatís possible. I have done that to a few older Yamahas I worked on.
Good luck with your new project
Last edited by Tarzan; 02-04-2019 at 03:10 PM.