Fuel filter may be plugged or fuel water separator my need to be drained. My last boat was a 2001 Challenger 1800 with the same motor and had a problem similar to yours, changed the filter and ran great after that.
You will need a special Seadoo diagnostic tool. Candoo Pro is a diagnostic tool that plugs into your computer module and will read the hours and will also read fault codes so you can do repairs yourself. It's available on ebay for around $400 but will pay for itself if you can do repairs at home vs. taking it to a marine mechanic.
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