How do you un flood a Jet Ski motor?

As quickly as possible, get the ski out of the water and get the drain plugs out.

Check for any other issues such as water in the electrical boxes. If you find any, do a quick job of drying them. You can go back and handle possible rust later. You don't want to waste time on that while your $2,000 engine is rusting.

Remove the spark plugs.

Crank the engine until no more water comes out of the holes. Make sure to let the starter rest between cranks so you don't overheat it (10 second crank, 20 second rest). Charge the battery as necessary to keep cranking.

Put the spark plugs back in. Get the engine running. Let it run for a few seconds.

Get the jet ski in the water and ride it for at least 20 minutes. Make sure you get the engine and oil hot enough to force out any remaining water.

After removing the jet ski from the water, thoroughly dry the interior of the jet ski. Apply a thin layer of fogging oil or wd40 to the engine to prevent rust. You may wish to spray some fogging oil in the intake to protect the engine. (If you're going to be riding it again shortly, you probably don't need to bother.)

It is critical that you get the engine running again as quickly as possible and run it in the water long enough to force out any moisture from the engine, otherwise the engine will rust and require expensive repairs. If you get to it immediately you can usually avoid damage.

Do not run the engine for more than 20 seconds without any water or more than 5 minutes on a garden hose.