I ended up attaching a script to my buttons to make it work.
In my button manager node I did this:
func set_button_mode( mode: int ) -> void :
#combat mode
if mode == 0 :
button_1.set_skill_shortcut(KEY_Q)
Then in the button script I created a method that would set the short cut:
func set_skill_shortcut( scancode : int) -> void :
var button_shortcut : ShortCut = ShortCut.new()
var button_event : InputEventKey = InputEventKey.new()
button_event.scancode = scancode
button_shortcut.set_shortcut(button_event)
self.set_shortcut(button_shortcut)
Seems odd that you have to create a shortcut inside the short cut... Yo dog, heard you liked short cuts...
Any who, it worked!