Why would you want to? The components are design to be interfaced from the JTAG port. Replacing the JTAG port with I/O pins that duplicate the function of the JTAG port is not very productive. You can control a USB-Blaster directly using FTDI's D2XX driver, so if your argument is that you want "total control" of the JTAG interface, I can help you with that.
Read these:
http://www.ovro.caltech.edu/~dwh/correlator/pdf/vjtag.pdf http://www.ovro.caltech.edu/~dwh/correlator/pdf/altera_jtag_to_avalon_analysis.pdf http://www.ovro.caltech.edu/~dwh/correlator/pdf/altera_jtag_to_avalon_analysis.zip Cheers,
Dave