I have a few ideas however I have no engineering background and only have about 30hrs on the meter riding time, take what I say with a grain of salt. I however grew up with two strokes racing MX.
Mechanically controlled water injection:
TNT makes and sells this
Back in the 90s apparently ECWI (Electronically Controlled Water Injection) was quite popular as it allowed the rider to tune the pipe through the entire power band, essentially changing the length of the pipe by slowing the sound wave down for low end grunt and modulating the water to have the ideal perceived length for the entire rpm range. It did this through a microcontroller that was tied into the ignition. It would then send a PWM (I think) signal to a pressurized water line that is attached to a solenoid to meter water flow at that spray bar. Through a series of dip switches you could control the different injection points on and off points in the rpm range as well as some other goodies. These systems were however quite unreliable.
My idea would be to use a mechanical system that is based on pump pressure using various flow control valves, injection points, and pissers to raise, lower, and cut off the stream at the proper point in the rpm range. These flow control valves would have to be user adjustable and easy to understand (ECWI is sort of black magic). I also think that the input line to the system may need to be user adjustable to account for total pressure as well as pump performance, possibly electrically, tied to the ignition to boost and lower the pressure, ensuring the correct system pressure is available to the the valves for ideal performance, if your testing deems it necessary. Additionally you may want to pick a popular pipe and performance test various locations to firm up your thesis with a dyno. Using a popular affordable pipe would also make it more accessible to the community (If you are going open source).
Waterbox performance, efficiency testing and design:
TNT makes and sells this as well. *claims 100-200 more rpms over stock
https://www.blowsion.com/blowsion-tnt-waterbox
Some waterboxes are loud, some are baffled, some are empty boxes. You could look into the effect of the waterbox, in multiple confiurations and sizes to try to find the ideal waterbox design. Not too loud, not too big, and one that assists the engine instead of hindering it. Possibly hook it to a dyno.
Sink-proof Scupper:
Home depot sells this. *PVC spring loaded check valve.
Scupper valves are great for getting large amounts of water out of your hull quickly by allowing water to dump right out of the back of the ski from the bilge. It does this with a one way valve that when floating is sealed however once underway with pressure from the water pressing on the valve from the bilge, and a drop of pressure from being on plane allows the water to exit at a rapid rate.
This design however comes with a large downside. When the ski is flipped upside-down (separated from rider) the air pressure inside the hull from the water coming in through the breathers opens the valve and the ski can sink rapidly. If there was a design that automatically and mechanically closed another valve when the ski is inverted it may not be such a dangerous design.
That is all I have for now. I may come up with more but these are ideas/questions that have been kicking around in my head for some time.