Lobbers:
All I did was to keep the original control box & wiring loom, you still need to select gears.
Disconnect the original throttle cable from inside the control box & fit a new longer throttle cable to the foot throttle.
Dont forget that the Yams require 'push' to accelarate as opposed to the mercs which require 'pull' therfeore the new cable has to be looped up around the front of the foot throttle. Most foot throttles will work in either direction with slight mods.
While you are doing this mod it may be worth wiring out the limit switch inside the control box to enable you to start in gear. Helps to prolong gearbox life.