Hi and thank you for your question.
It is a good thing that the engine in question still turns over. That does pretty much point to an electrical issue.
I am not clear if you "checked" or "changed" the fuse. If you did not change it, the only sure way to check it is to test it. You can either check it for voltage on both ends or with a test light. The point here is do not trust your eyes. This is by far the easiest and quickest check you can make and it would really be unfortunate to go through the rest of the electrical system only to come back to an open fuse that appears to the eye to be "good".
The next thing I would check is whether the safety lanyard, specifically the forked "key" is factory Yamaha. I have seen aftermarket units that flex too much and can cause similar symptoms.
Next on the check list is make sure the safety switch that is under the hatch for the cleanout plugs is being activated properly. They should be wired where the switch on the left controls the left engine and the one on the right controls the right engine. However, if someone has had them unplugged to remove the tray around the cleanout plugs, they could be plugged in crossed left to right. If you have 2 people available, have one person press the switch down as far as possible by hand and see if the engine cranks. Just in case the wiring got crossed, try both the left and right keys so there is no question you have the correct switch pressed.
If we still have a no start we are going to have to go into the electrical box and start checking circuits. You will need a test light and volt ohm meter. Are you prepared to do that?