Re: 1997 Waverunner 1200 will not start
I have the same ski and I also have a 97 gp760 that did similar that you're describing and I now am doing a top end rebuild on it. What happened was the oil pump driveshaft sheared in half and I lost oil to the cylinders. It would start up but barely and it seemed like it had no battery power which was false. It was due to the piston/rings trying to seize in the cylinder. So it was very difficult for the battery to turn over.
Might NOT be what's wrong with yours, but with the similarity, I had to explain what happened to me. You might check your compression in your cylinders to be sure.
Could also have blown your main 10A fuse in the control box.
Heck it could be several issues.