Thanks for your advise, I checked them out and they look good and I will keep that in mind, but as I have already spent more than I should I would really like to get this working ( so I can sleep at night)

I thought I would have another go at this. I checked the software info that came with the board and saw a configuration file for the mill. I loaded that and had a look at the pin configuration and found that they were all set to zero. I used that file to clone another plasma xml.
I opened Mach3 with this new XLM file and checked the pin configuration again and still the settings were all zeros. I tried using the keyboard arrows to move the motors and found that the X and Y will move no problem. The A moves with the [ and ] keys.

When I enter some gcode to test, like G0 X100 the X motor works fine, and I can reverse it also, same with the Y and the A axis, all work fine with either keyboard button control or gcode control. The problem I have now is that although I have A slaved to Y, it is not working, maybe I have done something wrong or not done something?
I know I could just use the A and Y as a single axis by connecting the stepper drivers together using the same DIR and Pulse signals and forget about A altogether, but I really want to have separate homing available for Y and A so that I can keep my gantry square.