If the hull is VERY clean, and it has a good trailer... it's only worth $500. The 1200 Yamaha engine is expensive to rebuild... and since yours is broken... you don't even have a "Good Core" to start with.
Unless you are looking for a real project... I would pass. Once you rebuild that engine... you may find that the CDI or stator is smoked... or it could have pump/cavitation issues.
A running mid 90's wave runner is only worth $1500 in good condition.
Last thing... since this is the end of summer for most of the world... prices on running skis is dropping. A member here just paid $2000 for a running '01 GP1200.