I would not attempt to fix the existing code. There are too many problems with the way the drivers were written which makes the probability of a successful and reasonably simple fix very low.
It looks like the controller uses very simple commands, although there is some inconsistency in the various subVIs. If you have a manual which describes the communication protocol in detail and lists all the available commands, it might not be too hard to write a new program.
The first thing is to establish the requirements for the program. Very explicitly document what it must do and under what conditions. How are the motor speeds/positions entered into the program? What controls does the user have? What actions are automated? Since you started asking about a stop condition: What is the maximum time allowable between the time the user presses the Stop button and the time the stop command is sent to the controller? Are there other time constraints? ...
Once you have the requirements and the controller programming documentation, then you can begin designing a program to meet those requirements. Without that information we cannot event tell you how hard it will be to get a working program.
Lynn
