FAdileh

Besides the filter you mention, there are small filters in the carbs themselves, and a mesh "strainer" in the tank  on the bottom of the pickup. The dealer should have replaced the internal filters- those dont normally come with OEM Mikuni kits, but they do come with other aftermarket kits.
Everything you describe sounds like a fuel issue.  The fuel pump is vacuum operated and integral to the magneto carb. Check the vacuum line going to the engine block and make sure its ok too. And clamped on each end. The fuel system from tank to carb isn't pressurized, as it would be if there were an electric pump pushing fuel from the tank to the carb. They would be under "suction" from the tank to the carb and pump- if they are standard rubber automotive lines they might collapse and block the fuel flow. The OEM lines are different, with a silicone outer shell and PVC liner-  somewhat stiffer than rubber lines.
I experienced the same issue with a Polaris after replacing the engine with an SBT reman. I also added a three outlet fuel pump, which sucked hard enough to collapse the automotive fuel hose. I replaced those with OEM type hose, and that cured the problem.
You never said if the engine shuts off instantly, or gradually. Define stall--
The next time you are out, gradually go up in throttle to the point where it would stall- pull the choke out some and throttle up more. If you can choke it / throttle it past the point of the stall, then the problem is definitely fuel related.

Thanks for the information. I will check the mesh strainer in the tank tonight. Hope this is the issue. The fuel lines are black Goodyear rubber lines. All of these lines were replaced about a month ago and they are in very good condition. No bends of any kind. They are heavy duty that it is hard to bend them.

Wouldn't you think that if there is a bend in the line it would not operate correctly even at lower throttle? I’m not so familiar with this but logic tells me that if the engine is starving for fuel it would go either way (low/high throttle).

The engine shuts off instantly when it stalls. Goes from high RPM with speeds of 40 MPH to 0 in ≤ 2 seconds.

I'm not sure if I will be able to do the throttle/choke test you asked me to do because the stalling occurs instantly. I'll be in the boat tonight, is there anything else you think I should check besides the strainer in the tank and the fuel vacuum line?

Thanks again for your informative and detailed help.

What shape are your fuel lines in? any sharp bends/ soft rubber?
What about the main fuel filter? Do the gauges cut out when the boat stalls?
Sounds like fuel starvation to me. Who did your carbs? Which springs were used for the needle/seat arm- stock or springs that came with the kits?

The fuel lines are brand new with the recommended ID. I checked for any bends and they look normal. You can see the fuel drip as expected through the clear filter.

My fuel gauge does not work and I'm not aware of any other fuel filter other than the small clear one prior to the carbs.

My carbs were rebuilt by the local Seadoo dealership and I'm not sure what kit they used. Knowing them I’m sure they have used OEM.

Why do you think the boat runs great for over 15 seconds at high throttle then dies all the sudden, then when I start it back up it idles low?