the control module is there to control the motor. so when the motor hits the limit switch for the 4wd postion in the t-case it shuts the the motor off.
Think of this way, if you wire a switch straight to the motor and remove the control module, when you flip the switch the motor will keep on going to 4wd low and lock up when it hits the end limit (where the motor cannot move the shift fork any farther) and sit there and stay energized and burn up. You could do it this way, you would just need to turn the switch off once it hit 4wd or 4wd low or else it would cook the motor (or continue on to 4wd low if you dont stop it in time to catch 4wd high if you want to use 4wd high, and then burn up if you left the switch on)
The module uses the limit switches to know which postion the t-case is in, and shuts the motor off once it gets there.
granted you could wire the tcase limit switches into your manual switch, but how would you be able to get the motor to operate again once the limit switch opened the circuit?....by use of diodes and/or relays. But if you got that in depth with it, all you would be doing is making your own control module/circuit. Which has already been done for you with the stock box so that seems like a waste of time to me.
Long story short, put the manual switches in connected to the original module if you like....but removing the control module, and making your own circuit seems like a total waste of time, unless you cannot find a affordable replacment for the module if it is already bad.
Welcome Visitor! Please take a few seconds and 
