Enabling USB communication with MAX II Development Board?

Are you referring to the PCI MAX II development board? I reviewed the usb_referencedesign example. It's not extraordinary instructive, but not based on auto-generated design files. Did you understand, that it uses a schematic entry (*.bdf) top entity? lpm_bustri isn't used as "USB transceiver" but simply the standard component in schematic entry that's available to interface the FT245 data bus. In a VHDL design, you would most likely use a behavioral description for it.

As a general suggestion, if you have difficulties to understand what the reference design is doing, design a VHDL interface to the FT245 bidrectional FIFO from the scratch, using the detailed FTDI datasheet.