You should only have one carb and they are really easy to work on but they have a small screen inside them that will collect gunk and not allow fuel to get where it needs to if they sit up for a while. Easy fix with carb cleaner and compressed air.
You can probably keep the oil injection if it has it. I would also check the carbon seal, which is the seal that keeps the water from coming in from the drive shaft. Check it for cracks. Also it might need a new wear ring, but you will be able to tell if it does when you launch it and try to run it.
www.sbtontheweb.com is the spot to go for aftermarket waverunner parts.
Those engine's are pretty solid, I ran the hell out of a '97 718cc engine. it sunked a few times and just kept on going.