What do you mean by "bogs down"...
Is the engine bogging or do you mean that the seadoo itself fails to accelerate when throttled.
The fact that you had the shaft etc apart leads me to believe you have not put something back together correctly or you have a wear ring or sealing issue.
I'm not sure about the older models but on my 95 there was a neoprene seal between the jet pump and the hull that was missing. The engine would rev and work perfectly but the water would not get directed into the jet pump. Instead, much of it would escape through the gap where the seal was missing. This can also happen when your wear ring is worn (water can escape around the edge of the impeller instead of being directed through it). Ultimately the lack of a proper seal or tight wear ring tolerance prevents the seadoo from accelerating. I know I could barely tow my 4 year old in a tube. Once I replaced the wear ring and added a new seal, she was a different animal.
If you issue is the engine itself failing to rev/accelerate then start with the fuel delivery system (carbs, filters, fuel lines) etc.
