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When playing the game, if you press F1 it will bring up a window which will let you change the default keys. As for the run when a button is held part, there are tutorials on here for that. The quick unequip would require an edit to Scene_Equip.
You could go through all your scripts and replace all the Input.trigger?(Input::Blah) lines so they have the correct input. I'm sure there's an easier way, but I don't know it.