1- You can make a tunnel paying a ruby and a room paying two rubies. Is it safe to assume you can make a room out of a tunnel for one ruby?
2- Does the stable in a forest count as an occupied space?
3- About the Food Chamber Tile. Does it take into account the unharvested veggies and grain?
1 - Two rubies lets you place a cavern tile on an unexcavated space. You cannot place a cavern tile on top of a tunnel at all. From the rules (with emphasis added): 'you can spend 1 Ruby to get a single “Tunnel” tile or 2 Rubies to get a single “Cavern” tile. You have to place it immediately on an empty Mountain space (adjacent to your cave system).'
2 - A space in a forest with a stable does not lose you a point at the end of the game. From the rules: "Count the number of spaces on your Home board that have no tile or Stable on them. You lose 1 Gold point for each such space."
3 - Yes. From the Appendix: "the Food chamber will be worth 2 Bonus points for each set of 1 Grain and 1 Vegetable that you have in your supply and/or left on your Fields."
Edit: added rules quote for #1.