Building cable for AX3500

I am designing an AGV that will use a AX3500 controller to drive the front and rear traction motors. Each motor has an 12 break. I do not have yet the AX3500. If I connect the serial cable provided with the controller so I can use RoboRun, I will not have access to Output C that I plan to use to release the breaks. Can I make my own cable using pin 2,3 and 5 for serial communication with Roborun and pin 1,9 for my break control?

No problem with what you suggest. Even better you may want to use first a male D-sub connector 15 pin with solder cups inserted in the controller connector, then solder into to the various pins you want to use and once you are satisfied you go with the cable.