Not familiar with the board- but if it has an existing USB port, does it also have a dedicated UART chip? I have made an FPGA based board controlled through Matlab using a USB -> UART chip, which seems to be a lot less effort than making a completely FPGA based USB interface (manufacturer provides drivers etc so nothing required PC side). On the FPGA all that is needed is an asynchronous serial receiver- there are several modules I have seen floating around the web you could use for this.