Did you try this. I do the same thing i use focus settings i actually under general tab for all my characters have a multiple of focus macros. So whenever i go ahead and change out one i just swap that macro. For instance i do this F8-F12 are my pip swap and change focus.

Toon A F8 /focus main /assist focus
Toon B F9 /focus Shaman B /assist focus
Toon C F10 /focus Shaman C /assist focus
Toon D F11/focus Shaman D /assist focus
Toon E F12 /focus Shaman E /assist focus

Ok say i want to switch out an alt for Toon D with another toon. You just have another macro on each toon set to this /focus dk1 /assist focus. So all you have to do using the focus macros is just switch out for macros and bing. All macros already say /cast [target=focustarget] spell. So you just switch out the pip macro for that toon and everything works out smoothly. I hope this helps in anyway.