I'm assuming this might be a fuel injected outboard since you quickly identified the cylinder misfiring.
1. Compression test of all cylinders to make sure they are within spec and within 10% of each other. No reason to go down the fuel and ignition diagnosing rabbit hole if you got big compression issue with #3 cylinder.
2. If compression is good, swap spark plug. Does the issue follow the spark plug? Use a spark gap tester and make sure the spark is jumping 7/16 distance on cylinder #3 spark plug wire. If it doesn't, then you have a spark problem.
3. If no change and the spark gap tests out good, swap with a good ignition coil and wire with another cylinder. Does the issue follow the coil?
4. If no change, swap the fuel injector that supplies that cylinder(s). Does the issue follow the injector?
If for some reason this was carb engine and the carbs were the exact same part, same jet sizes, etc., you might be able to swap it with a carb feeding the good cylinders and test for the issue again.
Some experts might have more specific advice, but might be worth having all the injectors cleaned out. Sticking/clogged injectors are probably the biggest cause of fuel injected 2 stroke outboard failure requiring powerhead rebuild.
If all of these tests come back good, I would be checking for intermittent ignition problem. A free troubleshooting resource for ignition and charging is:
http://www.cdielectronics.com/troubleshootingguide/
If it was a fuel pressure/delivery issue to the injectors (or carbs if carbed), that would probably show up on more than just one cylinder.
