I haven't done this yet, I'm about to get started on my mill again so I'll be able to help you in a week or so. You would think that shorting the two pins would be enough. However, it looks to me that you have to supply your own voltage. It would make no sense to supply an internal voltage to an isolated input. As I read the manual, the resistor is in series with the optoisolator to provide over-current protection, not as a pull-up.
Now that I read your post again, this is your problem. You need to supply a voltage (through a resistor to protect the power supply) to pull the optoisolator high.