As Rampage said for the most reliable is to leave it stock. Rotax engines put out more HP per CC then any other PWC engine. The manufacture has already pulled out the most power you can get and still maintain reliability/longevity.
That said with a 787 engine you can have the head shaved down just a little to increase compression to about 160PSI, you would still be able to run 87 octane pump gas and gain a little bit of power, while not affecting reliability much if any. You can install aftermarket flame arrestors, a better/aftermarket scoop grate, better/aftermarket prop.
Those items will greatly improve ski with out affecting reliability. Beyond that there isn't much else you can do with out increasing stress on the engine/driveline and reducing reliability.
-TheChad