1. if your back yard is fenced then it should be okay for her (no other critter able to come in and leave "deposits"). No public parks/places or contact with other dogs until she has had all of her shots (16 weeks or so).
2. I left water out all the time for my boys and still do. At night they never had water available in their crate, but if they stopped to get a drink coming in from going potty then that was okay.
3. Crate size is good and as for the bed being removed, I had to do that too, but I would leave some towels or blankets that are easy to just throw in the w/d in case she gets a little cold. My dogs were never snugglers under blankets but they like to wad them up and sleep on them that way.