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Mine did the very same when I left it sitting in the garage with dog day hot weather and the alarm was set all the time. Battery drained down some and first ride out of the barn was a bit painfull!
Recharged the battery and keep on tender all the time in the garage and have not had problems since.
The bike goes in tomorrow morning. I changed the plugs. It ran a bit better, still a bit rough and then the engine light came on. I was hoping it was going to be an easy fix.