I'm assuming the carbs and compression have been totally elliminated from the dead cylinder issue...so...
The 2000/01/02 SRXs and all the Vipers fire the plugs individually at a precise time. If everything is wired correctly then the stator,pickup coil,flywheel,coils,sparkplug, and CDI look after the spark + its timing
If you are getting strong, properly timed spark on two cylinders then the only components that can effect the spark intensity and timing on one cylinder alone would be:
-the flywheel[triggers the pickup coil[
-wiring to, and or, that cylinder's individual coil
-spark plug wire ,and or,plug cap
-sparkplug
Its always like being a detective...systematically elliminating the suspects
Bob