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I'll throw out some guesses:

Still sounds like a bad plug not firing............I know you've changed the plugs, but this is THE most common problem for this model ski, so you might want to do the plugs one more time just in case. When you pull the plugs look for a wet one (unburnt fuel).

Could you have bad gas? Have you tried higher octane? Have you tried a fuel injector cleaner (Yamaha makes a good product called Ring Free Plus, Seafoam is another good product)?

There are small fuel filters inside each injector. You have to remove the throttle bodies and the fuel rail to get to them and clean them. It is also possible for debris to clog the fuel pump or the check valve (see below for checking fuel pressure).

Don't discount the air filter as a problem just because it looks OK. Even a little contamination of the air filter can lower performance. Take it off an run the ski without it to see if there is an improvement.

Have you checked to see if you have spark on all cylinders? Sounds like one cylinder not firing (bad coil?).

Have you got good fuel pressure from the pump? Difficult to tell without a special gauge (should be 46-47 psi). You can remove the hose and hold it horizontal and crank it to see if you get a good stream of fuel out of the hose as an estimate.

I still can't explain the increase fuel consumption, unless there is a problem with the throttle assembly or a fuel injector, or you are just pumping unburnt fuel through one cylinder.
 

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Have you taken off the intake grate and checked the pump for something that may be lodged in there?
 

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You are right, even small dents and dings in the impeller can cause cavitation and reduce performance. Just as important is that the impeller needs to fit very tightly inside the housing (.35-.45 mm). You should check this clearance with a feeler gauge at each blade. Be careful smoothing the blades and the inside of the housing if it will cause the gap between the impeller and housing to increase, since you will end up loosing even more performance.

You may very well need both a new impeller and a new housing, or I'm pretty sure that you can get a plastic wear ring to go in the housing for your model that would be a much cheaper solution, and will give you a very tight fit between the impeller and ring. The plastic wear rings also offer some measure of protection against debris, in that the cheap plastic gets destroyed instead of more expensive metal parts.
 
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