When I started a new team a while back I had more or less the same problem, with one big mess of UI settings and keybindings. I solved it by:
- Reset all keybindings,
- Remove WTF folder
- Clear ISBoxer config (after making a backup ...)
- Setup ISBoxer like a pro,
- Manage keybindings from ISBoxer (created a macroset for each class, containing a macro for each spell, keybound to num N),
- Start wow and use Ualaa's suggestion (turn on broadcasting and configure all addons for each character at the same time)

By moving keybindings config into ISBoxer you get a much more pleasant interface for managing your macros and keybindings, and it makes it easier to change something for all members of a certain group (class or role, whatever).