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On my '96 VT1100 ACE, a non-firing cylinder came from a clogged pilot jet, and perhaps other carb. issues. It might be worth pulling the intake air ducts and seeing if a bit of starting fluid gives clarity.

Also, be aware that the two plugs for each cylinder are connected in series. A bad connection at the plug cap, a fried resistor in the plug cap, or even a plug that's gapped too wide, can stop the whole show, sparkwise. This also means that testing for spark is a bit of a PITA. The high energy spark system isn't supposed to be run into an open circuit. Test for spark, with both plugs inserted, and a spare plug with solid ground to the cylinder under test. Even better, use an inductive pickup, like a timing light.

Check the high voltage wires.
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