We have working example for FX3 CYUSB3014 with AN65974. But, you can port this firmware to support 16 bit GPIF. You will also need to modify the FPGA code to 16 bit parallel. Please note that you will need to assign the control pins as per the new pin mapping in the FX3. Please let us know if you have questions regarding this implementation.
I have a similar application, my application is xilinx FPGA to cyusb3035. the power to cyusb3035 is applied by FPGA except for VUSB. I uploaded firmware created with cyusb3014 to RAM and SPI flash without any error. My cyusb3035 is not responding to my parallel data and controls. What's the difference between cyusb3035 and cyusb3014?