The option for flashing in the eeprom is -f, I'm using this command:
openFPGALoader --unprotect-flash -c ft232 -f Lcnc.bit
So if I remember correctly, J9-1 and J9-2 are step and direction of stepgen zero for your confiiguration.
Do you have a multimeter to check if the board is geenrating any voltage on these pins?
I would start with the simplest configuration possible:
Use HAL.hal in support files, use halshow to check the pins status and set them manually. Start first with the board enabling sequence, as expained in the readme, then adde all the pins and parameters of the stepgen 0 and if everything is right once you set the velocity command to a value other than zero you should see the position feedback in halshow change and see the pulses on the pins. If there are no pulses but the position is changing then maybe there is some problem in your pin mapping.