This was a very great question, I don't think I've seen posted before. The 787 is my fav engine. Everything Dr. Honda said, is correct. There are ways of pumping that engine up, but not with a supercharger.
When Rotax designed this engine, they had high performance in mind. They patented the RAVE valve (which you see other jet skis use now) to create extra horsepower without increasing piston stroke or size. Where else can you find a motor that weighs about 80 pounds, that puts out 110 hp?
Lets just say you could supercharge this motor. You'd have to change everything inside it. I don't even know if the aluminum block could withstand the pressures. Piston, rods, everything. And of course, without intake and exhaust valves, with the coil designed to fire to both cylinders at the same time, it is just not feasible. You'd be better off to buy the 4-TEC motor and trying to figure out how to put it inside your ski.
Now, there are things you can do. I usually always recommend starting at your pump first. The motor creates great power on its own. On my 97 GTX, I have recorded in my info center, as my peak speed, 63 mph. Yes, we all know the dream-o-meters are not accurate. The only thing I have not stock is my impeller. I'm using the Solas Concord. IF you looked at the other pump additions, like a wedge or extender kit, you'd see more power. The extender kit would allow more of the ski to break contact with the water. Less friction means more speed.
There are several sites out there designed to help potential racers build their skis for racing. I'm to old to race and my ski is plenty fast enough for me to do what I like to do. We have an area at our creek, that is about a mile and a half long, about 15 feet at it's widest point, loaded with turns from left to right. We call it our slalom run. It's so awesome to run it. One wrong move and your in the woods. We have a person at the other end who clocks you, since only one ski at a time is allowed through, then we compare times at the end of everyones run, then give out the money. Oh yeah, there is a 5 dollar entry fee to play.
Lastly, like I've said a million times over. If you build your motor, all your doing is decreasing the life span of it. I have a 787 over 10 years old and still running at 130 psi of compression. Because I take care of it. I also use 100% synthetic "Quicksilver" oil (no TCW). I've used it for over 5 years, with no ill affects, plus my RAVE valves don't require as much cleaning.........
So, build your motor if you must, or just enjoy it for 10 years or so, and build your pump end........