SCARA robot Code

Hi,
I'm currently working with an Adept Technologies SCARA robot. I am running into trouble with utilizing a tool that is mounted one the
second joint of the robot, not on the third. Giving no rotation to that tool does not allow the controller to properly recognize where it is in the real world.
Does anyone have the resources or know somebody who can to tap into the CX controllers actual runtime functions.....or know how to view and change the code within them????
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