Here are my thoughts on the subject:
1 - I believe the FTDI chip on the BeMicro gets all of its startup information from the little microchip EEPROM on the board. You could just copy the contents of that EEPROM and lay down a circuit with the FTDI chip identical to the BeMicro board.
2 - See if these help:
http://www.ixo.de/info/usb_jtag/ http://openocd.berlios.de/web/ 3 - One of our software guys here wrote his own little programmer for a cyclone III using the FTDI chip. He doesn't use JTAG mode though and it's not compatible with the Altera programming tools. He just basically bit-bangs the serial programming pins on the Cyclone III with the FTDI chip. It's actually significantly faster than JTAG mode.
Jake