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OK, not familiar with just which cylinder is cancelled out by the vacuum switch. How did you disconnect it? Did you disconnect the knife connector on the lead coming out from under the mag plate? Or, did you just disconnect the lead from the vacuum switch?
How is it you have determined it is #2 that is misfiring?
I would run in at dusk using a timing light or those inline neon testers to ensure you actually have an ignition issue, and on which cylinder. Keep in mind that a shorted/fouled plug will lower the secondary voltage enough so the timing light/neon testers will show a “miss”.
PS: Forgive me if you have already described your testing procedures, I will try to review this post.