Thanks for the additional information.
The overheat sensor only limits peak RPM. It is what they call a "return to port" feature where it will continue to run and not leave you stranded at sea. Unlike a motorcycle where you can get off and walk, such is not the case with a watercraft so they have to include a return to port feature. So even if the overheat sensor has completely failed, the engine will start and run, but not exceed 3500 RPM's.
The meter is turned on by the stator producing an AC signal on one wire to the display. At this point, I don't suspect the meter is causing the no spark issue and tend to lean towards getting the engine running and see if the meter operates normally once the engine actually starts.
If you want to get some idea of the battery condition, do a voltage drop test on the battery. Connect your DC volt meter to the battery and hit the starter button. Read the volts it gets pulled down to. It should not drop below 10 DCV.
I was agreeing with your assessment that more than likely it is the CDI because you have no spark on any plugs. If it were no spark on one out of three, then we would look for something unique to that one cylinder. Considering it is all 3, we start thinking about what is common to all three that could cause the problem. Although it is improbable that all 3 pickups or ignition coils failed, it is possible. Check the charge coil too. It looks like that is common as well.
I have seen engine stop switches create issues as well. As previously stated, unplugging that is the best way to test it. If you get spark with the black & white wires disconnected (under hood), the start stop switch is bad. You can take it apart and inspect it and decide if it is salvagable or not.
To directly address the issue on the CDI, it is almost a process of elimination, If you have everything else on both sides of the CDI checking out OK, it doesn't leave many options. You can put a test light in the leads out of the CDI going to the coils, which would be Orange, Wht/Blk, and Yel/Blk (one at a time) and spin the engine over. If the light flashes, you probably have enough CDI output to fire the coils. Yamaha does give a peak voltage spec of 95.5 closed if you have a peak reading volt meter. The test light is pretty darn reliable as an alternative.
You can check the CDI output going to the primary sides of the coils, but beyond that, it becomes academic. It is not user servicable so if it isn't sparking, it needs to be replaced. There used to be after market CDI boxes available for it. I don't know if they are still available or not. Usually after market is less expensive than OEM.
One other thing I remembered too is if you end up replacing the CDI, make sure you get the updated bracket that has a stay that links the Electrical box to the cylinder/head assy. to help prevent some of the vibration related issues. They used to have a kit to update the early 1100's that came without them, and the later 1100's came from the factory with the stay equipped bracket. The bracket I am talking about is the chrome bracket that the high tension spark plug leads pass through. Just take a look at it and see if it has a leg that T's off of it and bolts to the cyl/head assy. If it does, you are ok! If not, it is worth updating it out of your pocket so you don't eat another CDI, or eat the first one if that is not is what the current problem is.
Another one last thing, , I also remember a tech bulletin Yamaha put out on the 1100 CDI boxes. They had a small zip tie around a bunch of wires right where they exited the CDI box. The bulletin said this put too much tension on those wires and could cause a failure (broken wire internally) so if you replaced the CDI box, DO NOT replace the zip tie. Also, if you do have to replace the CDI box, I strongly suggest taking some digital pictures of the wiring as you find it. It comes apart in about 3 steps and I would take pictures of the wires at each step so you layer them back in the way they came out. If you haven't seen them yet, you are going to be astonished and impressed at how many wires the factory could get into a very small area.