As far as the hard to start issue goes, my recommendation would be to start with the plugs. NGK BR8ES plugs are what I personally use(local auto parts store will have in stock typically-buy 6 or so always good to have extras on-board). You are dealing with a 2-stroke and if you know 2-strokes, they foul plugs very easily. Pull the plugs and look at the electrodes. If they are black/carboned up or are soaking wet(oil and fuel), throw in a new set of plugs. It is very possible you may need to re-build the carbs. What color are the fuel lines? Sea-Doo used a gray colored line for a while which did not hold up very well. The inside of the hoses would get soft and you would end up with junk in the carbs. The needles and seat are also known for going bad.
Without being able to see whats going on when you try to take off, It is hard to tell what is going on. Remember it is a Jetboat and you are using water to push the boat out of the water or through. It typically will not be "crisp and quick" about a 3-4 second time to get moving is normal. Cavitating is when you get air going through the jet pumps and this in turn causes the efficiency of the jetpumps to go down(air compresses faster than water and when air is being pushed through the jetpump, less waster = less thrust blah blah and so forth)
As far as the RPMs not matching, give me some more info... do they idle at different speeds, when you listen to the engine can you tell one is running at a higher RPM than the other? (you can determine this by adjusting the throttles until they blend together. They basically make a harmonic drone when they are close to the same RPM.)
