Check the compression using compression gauge.
Decide if you want to fill the fuel tank, or empty it for winter. Put some fuel stabilizer in the fuel tank, wash the stabilizer down into fuel tank with clean fresh fuel.
Start engine then turn on flush water from house and fog engine through carburetors with fogging oil, don't run more than 3 minutes on hose, shorter time is better. Turn off hose water and then turn off engine within 30 seconds. NEVER run engine more than 30seconds without cooling water. Always turn off cooling water first, before turning off engine, always start engine first, before turning on cooling water. Follow this sequence so water doesn't flood the exhaust and back up into engine cylinders.
Obtain some pink recreational vehicle anti freeze for the engine freeze protection and some 90 weight(marine type preferred, GL-5) synthetic gear oil for the jet pump rear bearing, there my be water in the bearing housing that can freeze so it needs to be emptied and replenished by removing the main nozzle from the jet pump and the black plastic bearing cone to check for water, remove three metric Allen head screws and four bolts holding the main nozzle, disconnect reverse bucket and steering cables using 10mm socket and box-ended wrench.
Drain the contents (a small volume of oil) of jet pump bearing housing and check for water(oil/water milkshake). Re-install bearing cone and pressure check if water is found, I like to pressure check to confirm bearing housing is leak tight after installing the bearing cone.
Freeze protection:
Pinch the engine drain hose(using large hemostat). Through cylinder head water inlet hose, pour antifreeze into cylinder head using funnel and piece of hose to protect if there's some water in there(there is always a small amount of water). Remove hemostat pincher and allow water/antifreeze mixture to drain through engine drain hose.
Pour some antifreeze into aluminum water box through hose connection at water box valve (~ 1 cup is enuff), to keep small amount of water inside water box from freezing.
Start engine for a few seconds and blow remaining water out of exhaust system.
Remove spark plugs and pour about 1oz of 2 stroke oil into each cylinder, turn engine over by hand a few revolutions to distribute oil. Install spark plugs.
Stop and have a beer with a ham sandwich and chips of your choice.
Remove bilge drain plugs from behind boat, unscrew them and leave hanging so rainwater can exit in case of rain. A boat can sink (fill with water) while sitting on the trailer.
Remove battery take indoors if waiting for spring.
Spray protective oil like CRC fogging oil over motor and electrical harness to prevent moisture damage and corrosion.
Enjoy winter, read over the owners manual and service manual, order a few parts, go snow skiing if possible and hug the family dog daily.
Prepare to perform preventative maintenance checks and procedures in the meantime.
Maybe someone else can add to this list.