How do you repair a transmission on a 1999 zx9r ninja?

The best way to repair a 1999 ZX-9r's transmission is to buy a good used one from a 2000 or newer ZX-9r and install it. The 2000 and newer is a much better designed unit and will not have near the problems as the 1999 unit. You can also send your 1999 unit to a reputable shop to have all the gears undercut but this is a much more expensive option compared to dropping the 2000 tranny in it.