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My 2004 BF50 is running rough. When I remove the top plug wire while the engine is running, nothing changes. When I remove one of the two lower plug wires then engine stalls. Does that mean my top cylinder is not firing (fuel and/or spark)?
Yes that is exactly what that means. So you already isolated your engine problem to the top cylinder not firing. Now you need to go further and test to see if you have spark on the top plug. A quick way to do that is to swap one of the other spark coils with the top one. If you now have the top firing then you have a bad coil to replace. If it still doesn't fire, then you have whatever feeds that top coil bad. It is a simple process of swap and elimination...
Spark failures on Hondas are extremely rare and carburator problems are very common. Your top carb is dirty and needs to be cleaned. Id clean all 3 while i was at it since they all come off at once.
