It has been a few years since I worked on this part of my Shizuoka, but I think this schematic should be good:
http://www.wallacecompany.com/machine_shop/Shizuoka/Bandit_Stepper_Driver.png

The pin numbers are in the hexagonal symbols on the left. The DIP socket is labeled as can be seen in this picture:
http://www.wallacecompany.com/machine_shop/Shizuoka/00001-1a.jpg

This is my version of the input circuit I made before I got the schematic:
http://www.wallacecompany.com/machine_shop/Shizuoka/Shizuoka_Step_Drv-1a.png

The first diode, such as D1, is for reverse voltage protection (100V) since the diode in the opto-coupler has a low reverse breakdown voltage (6V). R1 limits current. The 4N35 diode has a 60ma limit, but I would shoot for 10ma. The forward voltage drop for D1 is close to .65V, R1 at 10ma is 10V, the 4N35 drops 1.2V, so we need close to 12V for the On signal. I have been using 5V and it seems to work okay.

Since these inputs are already isolated, I don't use an isolated break-out-board, but just a buffer like this:
http://www.wallacecompany.com/machine_shop/Shizuoka/buffer-1c.png

A 12V buffer would be better, or replace the 1K resistors with 470 Ohm resistors, or piggy back another 1K.

My old configuration files show the HAL connections, which have most likely changed, but should give you an idea how it might be done:
http://www.wallacecompany.com/machine_shop/Shizuoka/emc2/configs/ST-N_current/

I used Stepgen type 9 for half-stepping which gives a .0005" step but also has lower torque for half of the steps. This limits the rapid speed, which I set by increasing the limit until I got missed steps, then I backed off a bit.

That is what comes to mind so far. Good luck. Please let me know how your project goes.