Well, most of those can be done by having the skill inflict a new state.
So, for instance, the default state ATK UP raises attack. So Focus needs only inflict that state. The same can be done for Protect, just DEF UP. Stone can inflict the state Incapacitated on an enemy, and that would be instant death. Further, you can set all of the skills that inflict these states to be usable only in battle - that's not a problem.
I don't know about the other two - might need a script if you didn't also want to raise the actor's magic attack as well.