Found this link that might be of some help to you...
http://www.marinepartsman.com/ELECTR...outboards.html
Specially :
"OUTBOARD ELECTRICAL & IGNITION TROUBLESHOOTING TIPS
1. Intermittent, weak, or no spark output at two spark plugs usually indicates a bad TRIGGER.
2. Intermittent, weak, or no spark output at all three spark plugs usually indicates a bad STATOR or SWITCH BOX.
3. Intermittent, weak, or no spark at any one spark plug usually indicates a bad SPARK PLUG, COIL, or SWITCH BOX."
So since you ruled out the plugs and the coils and only happens to one cylinder, this leaves the switch box like you said.