Spark?
I just did a little research in my shop manual and altough it only goes back to the 96 model, the information my be relevant to the 95 model as well. These boats were designed with the idea that they could become water flooded. So there is a great possibility that your electrical problem is minor. How long was it under water? This would be the first question because although the electrical systems are sealed, I don't think they can stay submerged for a long period of time without seeping into the system. I don't know about swapping electrical systems from a PWC to a sport boat.
Looking at the electrical system to the 96 model, it has the magneto driven electrical system with a stator plate. If this had no water damage, I'd check the coils and also any fuse links along the path.....Seadoo.com's parts list also dates back to the 1996 model. You may be able to look at the exploded view on that model to see if the system is crossable. I know this isn't isn't very much but I'd suggest that you investigate the current electrical system before entirely replacing it. You may find your problem to no spark as a small one, verses trying to completely change out an entire electrical system, especially if you don't even know if the engine is still in running conditioin.
I did just look at the 96 system again and wonder if when you attach your lanyard, do you hear any beeps. It looks like this model is equipped with the DESS system, (digital electronic security system), and a MPEM, which is the electronic module. It may be worth your effort to order the repair manual for this model. I believe it's available through this forum site for a really good price.