S3 dev kit - using the USB for general purpose I/O

Hi

I have a Stratix 3 dev kit. Can I use the USB for both programming the Stratix (or maybe the flash) and then, once the Stratix is programmed, hijack the USB for my own general purpose data I/O? Unfortunately, project constraints mandate the use of USB, not ethernet.

I have tried to implement this already, but I have hit a snag. Basically, there is a MAX2 sat between the USB and the Sratix. There are two USB phys, a Cypress one and an FTDI. The MAX2 is talking to the Cypress chip, not the FTDI. If I reprogram the MAX2 with a USB pass-through design, I lose the ability to program the S3 via flash and USB. I now program the S3 and the MAX2 via a JTAG cable.

Has anyone used the USB for both programming and general data I/O? If I add the Altera PFL to my MAX2 "passthrough" design, would that be work?

Thanks in advance

Ian