Personally I hate running, but that's me. 3 months is more than enough time to train for an event, so I guess it's just a matter of what you want to do.
I'd like to say that if you concentrate on running and keep mixing some rides in you'd be fine to hit the winter 50 milers, but I know nothing about how running training converts to cycling. Seems to me that cardio endurance is cardio endurance no matter how you get it. You gain effeciency and muscle memory by concentrating on a specific discipline.