Yes, as long as the stone is compatible with the species, characters with multiple lv. 100 Pokemon of that species may equip or switch the stone between either as they please. Of course, that said, the other limitations are still in place: only one Mega Evolution per battle, and after an individual Pokemon has Mega Evolved once, they won't be able to do so again until the next day!

As for the candy, it'll be an IC surprise! Nephilis was in too much of a hurry to leave any detailed information about his gifts behind!