We have a reference design using FX2LP to implement a USB 2.0 to PATA interface:
So your design is applicable. However, FX3 has a GPIF II interface which is different than the GPIF interface of FX2LP. So I' m afraid you'll have to build your own code.
I recommend you use FX3S if you want to design a USB 3.0 to SD card application.