The problem you're going to run into, may be mix matched parts. The 951 is already one of the most tweaked engines from the factory, with an expected life of 200-300 hours. (10 years).
With a 100% factory setup, I can tell you how things should go, but I'm going to sound like a dealer and say... return it to stock...
But, in the mean time, I'd check your air/fuel mix, by googling, and learning to read spark plugs. That should go a long way.
#1 is compression - without that you have nothing. a 951 should read 110-130 new, the important part is that both cylinders read the same. not the actual number... (long as it's not like 10!)
The TPS - Throttle Position Sensor is under the oil tank. it sends 5v to the MPEM (I think) below 80% throttle, and 0v above that (possibly the other way, it's been a few years).
the RAVEs are the black round things held on by 2 6mm (maybe 5mm) bolts on each piston, they change the exhaust valve height, they open to give you more top end. there is a hose that goes from under the engine (above the starter I think) that goes to a 12v solenoid just above the water out on top of the engine. there should be a grey 90 elbow there. Verify all the hoses are good, not leaking, and not clogged. also applying 12v to the solenoid should give a solid CLICK noise.
in the back of the ski, on the 'muffler' (water box) there is another RAVE valve that likes to leak, this one restricts water at higher RPMs to give you more power. verify it's operation... usually remove it, see how it works, and blow into one end, while moving up/down. should open/close with exhaust pressure.
if the prop was bad- usually has the opposite effect - pushing less water = less load on the engine, allowing it to spin up with little movement.
Without the stock airbox, you've raised the air pressure into the system, with the engine not having to work as hard, the carbs would have to be adjusted. Basically the opposite of a choke.
If you hit 6k WOT, pull the choke just a little bit, see if your RPM goes up or down. With the restricted airflow, it should be forced to pull a bit more fuel. If that works, it means you're running lean, and don't have enough fuel to hit full power.
7k is a 'best case scenario'... ideally aim for 6800... and call it a day.