Just an fyi - Jet-n-cat can have different specs for the motors from Yamaha, although often times the specs are same.
Since a jet boat can be run full throttle for LONG periods of time, internal cylinder cooling at WOT needs to be a double-check area.
Unless there is a forced water cooling restriction(weeds/sand), you should be fine as she was factory delivered. Idle RPM needs to be 1250, so the pump can circulate cooling water. Running the motor at lower rpm is very convenient for docking, etc., but it will overheat the motor - don't do it.
The Waverunner plugs used are BR8HS. B8HS can also be used, but you will get "noise" over the radio, etc.. Gap is .024. #8 heat range plugs are reasonable. There may also be a plug sticker on motor or area.
Carbs settings...All low/high needle settings are quoted as counter-clockwise turns out from a lightly seated position. I don't have the service manual in front of me...
Did you count where they were at when you rebuilt the carb? these should generally be fine tuned for peak performance.
For the low, set it at 1-1/16 turns out. For the high, set it at 2 turns out. The low is located low on Carb, the High is high on the carb.
The low is fairly easy to adjust when in water for smooth low end running and take-off and should ALWAYS be fine tuned before the highs.
The high speed adjuster provides the all important extra fuel at WOT settings to keep the pistons from melting down, so they cannot be arbitrarily leaned out.
Running too rich (2 turns out should be a tad rich), may not be fastest, but is a good start point.