Funny you write this. Mine does the same thing which is new over the past week, and this is the first time I have ever filled the tank to the very top. This weekend before it goes back out I am cleaning my plugs just to make sure they are not fouled, as well as checking my fuel filter and possibly cleaning the power valves which is easy I hear because they can stick (my oil pump was disconnected when I bought it, which is getting replaced and hooked up by me as a winter project - and when I say power valves I'm talking about the the exhaust valves - at least I think this is what they are called - new to this). In addition I have gotten gas the past couple of times where I normally do not, and have in the past suspected bad gas there (happened about the same time my bog issues started). I believe in starting with the easy to look at basics first and go from there....... also a few other notes ----- I'm sure you are using above 91 octane.. I have a 1200 Kawasaki Ninja and anything under 93 makes it cough and choke and bog, these Jet ski's are the same. sorry just reread the beginning.
I also am at the moment running TWC oil mixed in the gas (which has been temporary, and am switching to XPS type oil - which I believe is the oil I should use because TWC oil will shorten the life on the Sea Doo jet ski's - please if anyone can verify this that would be awesome - looking through threads now for that info).
Thanks sorry such a long note.