Did you manage to work out the wiring for the machine?

Have you got any photos of what BOB (Breakout Board) is fitted?
My suspicion is it's possibly a chargepump config issue.
The chargepump needs to receive a fixed frequency signal from the parallel port, otherwise it won't allow any of the outputs from the BOB to enable. It's a safety feature to avoid any 'random' movement/activations caused by uncontrolled parallel port outputs, which can happen as the PC hardware gets configured as the PC boots.

However, the fact the E-Stop light goes off during booting, may mean it's using a simple enable output.
Some photos of the inside of the control box would be helpful.