The first ride of the year is when a ski that was parked in good shape is found to have one thing wrong, usually something small. A scan before the first launch costs very little and gives you a chance to find that thing on the trailer instead of in the middle of the bay. This works on every four-stroke Yamaha the M-JET Diagnostic supports, 2002 to today, with the dongle in the diagnostic connector and the app on your phone.
Read the old entries first
The fault memory remembers the end of last season. Before the ski sits and before you clear anything, read it and write down what is stored. An entry from September may be the explanation for something you meant to look at over winter. Some entries are sporadic and others are just stored, and owners say a check engine light can also disappear by itself after several start and stop cycles without the fault being fixed, so an old entry deserves a note even if it looks harmless now.
After you have written it down, clearing the memory is reasonable. If the same entry returns on the first ride, it was real. Clearing the fault memory describes the sequence.
Battery before everything else
A battery that sat all winter may be weak, and a weak one makes the control unit log faults that have nothing to do with the named part. Look at battery voltage in the live data with the engine off. Charge the battery fully if it reads low, and read it again. Later, with the engine running and water supplied, check that the reading rises clearly above the resting value. A charging voltage that stays flat suggests regulator or wiring trouble, including corrosion at the regulator.
Cylinders, one by one
Use the individual component tests. Every ignition coil and every injector gets its own test, plus the fuel pump. A three-cylinder ski has seven components, a four-cylinder one nine, and on the FX140 and FX1000 the two coils each serve a pair of cylinders, 1 with 4 and 2 with 3. If one cylinder doesn't respond, you know where to look before you are on the water. The pump test shows only that the pump runs, not how much it delivers.
Around the fuel system, keep the area ventilated and free of ignition sources. The engine itself must not run on land without a water supply.
Idle and the live values
Start the engine with water connected and watch the idle for a minute. On models with a stepper motor or bypass valve the idle is regulated by the control unit, and the app has an idle learning function that is worth running if the idle is uneven, for instance after battery work. Look at temperatures and intake pressure while it settles. Idle that surges or drifts is easier to see in a short recording than by ear.
Service reminders and hours
If you changed the oil, reset the oil change interval so the reminder starts over. On models that have them, the maintenance or flush warning can be reset as well. The service reset page lists what the app offers. While you are in there, read the engine hours and the hours per rpm band and write the numbers down, so next spring has something to compare against.
What the scan won't do
It won't tell you whether the plugs have seized in their threads, whether the impeller took a hit last season, or whether a connector corroded without ever setting a code. Those need hands and eyes. Check the plugs and the connectors by hand while the ski is still on the trailer, since a clean scan report is easy to over-trust.