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Sounds like you have something in the cooling system causing a blockage. On the FX models debris will sometimes clog the thermostat. It is a pretty easy fix, to remove the thermostat (on the right side of the oil tank) and clean it. There will be a cooling water line attached to it. Since yours is new, I'd take it back to the dealer and let them make sure all the cooling passages are clear. You may have sucked up sand or other debris.

Look at the intake grate and impeller area first to be sure there is no debris there blocking the inlet cooling passage. (I know you already checked, but look carefully with a flashlight. There is a little port there that may have something stuck in it).

That outlet on the left (port) side of the ski is for water over flow from the cooling system. It should not be smoke, but occasionally it may look like steam. The right side (starboard) outlet will only have output at high RPM.

Don't continue to run it until it is fixed. You are going to cook your new engine.
 
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