A hole in the exhaust will indeed cause backfiring; unless you have other problems w/ the mixture, I wouldn't change anything yet. And being flatslides, your carbs don't synchronize according to the vacuum each one "sees"; they are sync'd mechanically. Once set, it's pretty hard for them to "go" out of sync.
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2007 Multistrada 1100, Termi silencer w/DP ECU, DP hard panniers.
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