1) You can set up keyclone to "do not pass" WASD and whatever other keys you don't want to send to the minion version of WoW. e.g. I have WASD, E,Q, / and a couple of others on "do not pass".

2) If F11 is a macro on one char, and a macro on the minion UI too, it should complete the action on both. I recommend Bongos for toolbars and keystroke assignements if that helps.