Not sure I have an answer but I have a 2000 ZXi 1100 that just ate the middle cylinder. I have heard talk about the oil injectors going bad on these skis, which may be my issue. In your case I wonder if it could be a carb issue or plugged water passage? If its running lean, its going to run hot. Hope you dont have to do a rebuild!
97 1100 ZXI hot cylinder
I'm a newbie to this forum and checked some posts after my son swamped my Jet Ski (97 1100 ZXI). 
Got all the water out and the engine running, but it will NOT idle. It shuts down under a rough idle, or any less than 2500 RPM.
Noticed that only the front cylinder gets very hot after running for 15 minutes with cooling hooked to garden hose. I have two theories:
1. Cooling system blocked to front cylinder
2. Extreme friction in front cylinder causing overheating, due to ???, I'm afraid to ask and probably expect an engine re-build or worse.
Any suggestions from an experienced motor head?
Got all the water out and the engine running, but it will NOT idle. It shuts down under a rough idle, or any less than 2500 RPM.Noticed that only the front cylinder gets very hot after running for 15 minutes with cooling hooked to garden hose. I have two theories:
1. Cooling system blocked to front cylinder
2. Extreme friction in front cylinder causing overheating, due to ???, I'm afraid to ask and probably expect an engine re-build or worse.
Any suggestions from an experienced motor head?
