The machine runs the GRBL controller firmware. You will have to make GRBL work with the processor on the other motherboard, if possible. I think that there is a version of GRBL for the Mega (2560). Google should find it. You will have to set GRBL up to work with the other motherboard. That means at least changing the pins called for X, Y step and direction, pen up and down and limit switches as well as the other relevant settings. I think that, with a bit of work and research, you could get one of those boards to work.