I can help with a few here:
1. How long from Managua to Granada (and would you recommend a bus or private transfer?)
45 minutes via private transfer. Not sure about bus. I can recommend Paxeos private transfer service. If you are arriving at night, would definitely stick to private transfer. Paxeos probably won't have an English speaking driver, but they will have a sign with your name on it at the airport. You can book by email using English.
2. How long from Granada to San Jorge
90 minutes to 2 hours by transfer service. Tierra Tour service in Granada offers a shared shuttle that's a pretty good bargain. They have a location in Granada just down from the central park... in the direction of the lake. You Moon book will show it on the map. They speak english at their office location. I think it was 15 bucks. The bus is way cheaper, but the shuttle is worth it. By bus you make a many stops, and have to transfer in Rivas. If you're trying to catch the 1030am ferry, take the shuttle.
4. How long does the ferry take to cross to Ometepe - one thing I read said 30 mins another said 1 hour!
1 hour.
Don't know about the rest... hope others can help.
By the way... what happened to number 3!
