As I said- one possible theory. Not the plugs, but possibly no fire going to the plugs. It could also be any number of other things....
To check this put any good plug into the wire and turn over the bike while holding the plug next to the engine. In low light you'll see a spark on cylinders 1 & 3. How about 2?
Also, several of us have found that the plug wires are just resting on the plugs, not seated onto to them (from the factory). Mine ran like this, but I firmly attached them when doing my 10K mile service. It seems possible that if this was the case with yours that the plugs in #2 weren't firing because of that.
Lots of simpler explanations for the issue you are experiencing that, if I were you, I'd be exploring