What do I need to do after 10 years of storage.To put a 1992 Sea Doo in water?

Water could be getting into the engine from the exhaust system which may not be totally drained. Remove the exhaust pipe, remove the spark plugs and turn it over with the starter. Now drain the oil, replace the plugs and try starting without the exhaust - on land - briefly. Now check the oil again.
Water can only be coming from the intake or the exhaust so just keep looking for the source. Mine took quite awhile to clear but now works fine.

There's relays for the system located in covered fuse/relay box

These vessels have a kill switch with a cord that you have to wear on the arm in case you fall off. I would be looking for a problem with that kill switch

Pull the plugs and fill it with wd-40.
And whatever you remove just replace tightly.
Unless its a head gasket or gasket mated part, torque values aren't that critical . Too loose and they'll vibrate out. Too tight and you'll snap or strip it out. A lot of repairs at shops are seldom torqued it all goes by feeling and for the stuff that needs to be torqued like internal parts just google whatever part it is and the type of ski and it'll show in your search.

have you checked the intercooler isnt leaking water into the air intake while running ?

Take out of storage and float off trailer into water

po544 code is exhaust gas temp sensor functional problem ! is this in the water or on the hose pipe as hose water pressure may be low ? you can only run seadoos for 3min out of water on a hose pipe as the engine cooling system will overheat !

carbs need cleaning and check the pulse jet that squirts fuel on set off , fuel pump diaphrams ok ?

if you have one of the kill cords that is round and it snaps onto a round button that has a silver dot in the center that when the kill lanyard is snapped into place makes a connection to the silver part inside of the kill lanyard itself. most the time its because it is still verifying that it is the right key. they are programed to match you CDI box/ignition module of your ski. this prevents theft. if you clean both the key and the button the key connects to with some rubbing alcohol to insure a good clean connection will most likely solve the problem. when you put the key on the ski you should hear a beep then wait 5 to 10 seconds before hitting the start stop button . that gives the ski time to recognize the key is in fact the correct key to the ski.. hope this helps

sometimes altitude can make a difference, but most likely your problem is from storage. The air is thinner at 7000ft, so it will only be air mixture adjustment. You need to prepare your bike for storage! I would remove the carby, remove the bottom from it and inspect for dirt,and or water, clean the jets out, and put back together. The cause is most likely water or dirt in your carby.