Good points, light chop is generally best, even wax will slow you down if you are competing for speed! It's surface tension that needs to be reduced - by scratching the hull surface, actually (microgrooves).
Keep in mind however Yamaha jet boats' intakes are way closer to the middle of the boat and a stepped hull construction is not an option as it would case the pumps to ventilate/cavitate. Loading is a big issue, as the intakes are not at the stern like in o/b jets.
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100% correct. The intake and jet pump are the real limiting factor as it forces a large section of the boat to be in the water in order to make sure the power is constant. Realistically anyone attempting to hit the top speed of their particular boat really only needs to fight against basic Physics that every performance boat runs against.
1) Reduce as much weight as possible and position any weight on the boat as far back as you can without causing cavitation (balanced weight laterally as well)
2) Reduce the drag of the hull in the wateras much as possible (either out of the water or reducing the drag coefficient of the hull in water)
3) Be as aero dynamic as possible (Bimini closed, windshield up, driving behind the windshield)
4) Get the best conditions (Closest to sea level, cool air temperatures, low humidity, cool water temperatures, minimal breeze with a little chop on the running surface to break the water tension)
Finally, don't rely on the boat speedo unless it is GPS based. Even then if you're looking to be as accurate as possible, redundancy is your friend. Doing passes in opposite directions and taking the average can also help show how much wind, current and wave shape can affect speed.
You can follow that pretty much for any boat trying to get a max speed run and getting the best possible results. Coming from someone who has driven and been around speedboats for most of my life, these Jet boats are not ideal for anything really over 60mph anyway due to the laws of physics with the jet pumps. The acceleration and immediate handling response at speed is what makes the boats fun so don't worry about he top end too much