The last of the Yamaha two strokes (99-06) were the GPR 1200 and 1300 and the XLT 1200. These are referred to as PV skis because of the presence of power valves.
There are two key failure points on these skis that can be prevented.
1. The power valve mechanism can fail internally. The pin for the lever link falls out and can destroy the engine. There are two easy fixes for preventing this. Wave Eater makes a kit that fixes both the lever lines and the actuator couplers or SBT makes an upgraded lever link that has a pin retainer built in.
2. The second issue is that these are among the few, or possibly only, skis that had a catalytic converter. A 4″ thick ceramic screen-mesh in the exhaust which usually fails at about 80 hours. In a two stroke engine there is an exhaust pattern which flows out for a while and then in for a while, which means the failed bits of ceramic screen are sucked into the engine. Not Good.
The fix for this is easy. The D Plate Kit, which replaces the screen-mesh and fools the engine into thinking it is still in place. This kit comes with a bypass chip that plugs in where the cat exhaust sensor used to be to complete the job.