I really didn't think anyone would bother to steal a 18 year old ski.
Well then I think I would go for it. The 96GSX can be valuable as a parts ski for the body parts, I know I have one. It's the only year that SeaDoo used that color so body parts such as the hood, gauge cover, handlebar cover, rub rail, corners, and sponsons are all unique to the 96GSX. Actually I might be interested in a starboard side sponson myself, the one on my ski is the wrong color.
I don't know of any specific threads on changing a motor, but it's really not that difficult. Remove the pump, remove the drive shaft, disconnect the electrical, disconnect the hoses, remove the bolts to the motor mounts. I'm not sure if you need to remove the tuned pipe, I'm thinking not. Two guys can wrestle the engine out but I would use a come-a-long or engine hoist. I've got a couple of old spark plugs with washers welded to them to use for lifting, but you could just use a nylon strap.
The job should be even easier because you have a donor ski to use as a model. Good luck and if you need help just yell, actually there's guys on here with better mechanical abilities than me [MENTION=57920]racerxxx[/MENTION] is one of them. He's got several threads where he has restored skis that may be useful.
Lou