I believe your ski has two filters. If so you probably cleaned the filter above the gas tank (cleaning this filter at least once a year is a good idea) But you need to check the screen in the tank. It’s a basic screen filter that covers both the main and reserve tubes. I had some grit in mine once and could not get it clean. Bought a new one from the dealer (about $6) and my ski ran great. Good luck I hope this helps.
For you first issue the fuel selector valve needs replaced.
For the second issue SeaDoo carbs have a tiny filter about the size of a pencil eraser internally - it probably is allowing enough fuel thru up to almost full throttle. Due to the age I would recommend a carb rebuild consisting of new filter, diaphram, needle and seat, and popoff spring.
As EdM said, the selector valve is either clogged with deposits or has developed an airleak. The airleak is not uncommon but it's probably clogged with deposits.
You prolly haven't done the fuel line conversion on your ski have you? If you still have the original grey Tempo brand fuel lines, that's gonna be your problem. These fuel lines begin to 'rot' after a few years. The inner lining breaks down and travels downstream into the fuel selector valve and into your filters.
YOU NEED TO REBUILD YOUR CARBS NOW!! Sorry about the caps but I can't stress that enough! If you wait to rebuild the carbs, the inner filter thats the size of a pencil will starve the carbs for gas. When the carbs are starved for gas it creates a lean condition in the engine which will eventually result in a seizure or piston failure.
Easiest check: Pull the fuel selector valve off and out. Look in it and see if it's clogged with a greenish brownish gunk. That gunk is the remains of fuel line. Just clean your selector valve with carb cleaner and blow some air through it. It'll be good as new then!
While you're in there, you should go ahead an replace your fuel lines. If you don't you'll just have this same problem again later. For the replacement lines, just go to a car parts store and pick up 15 feet of 1/4" fuel line and 5 feet of 3/8" fuel line. Just get the regular fuel line, you don't need the stuff rated for fuel injection.