Have you started to create the game?
1. You can easily add a timer, when it goes down a certain of time, it sends out to change signals on your trees and it will grow.
2. This is very much like Facebook game, do you understand how they work between the server and the players screen? Because, to have the farms still playing when a player logs off, you need to have a server to be kept on for 24/7
3. Autosave, try this: scirra.com/forum/autosave-game_topic59531.html