Thanks for the suggestions. Most of those are already being worked one!
The message box will be separated in two Tabs: Game Log and NPC Chat. That should solve most of things.
Food Energy is what you use to actually heal HP and MP. You eat to get food energy, it consumes food energy to give HP/MP.
The game will also force a save everytime you enter a map with no battles on it, making those even more of a safe spot