Here is a brief update. I have looked at every connection and it all looks right. No unplugged wires, no broken wires.
With the right rear handle plunged directly into the machine everything on the handle works properly. If I plug it in through the compuquilter system the right rear handle no longer works but it does turn the top indicator lights on when I try to push a button. Also from the software when I try a one stitch, the lights on the top of the machine turn on but nothing actually happens.
I am not sure what else to try, any suggestions would be great. I will try to call into APQS in the morning and see if they can help further.