Hi
If you need the manuals I have copies, I am presently converting the Duet to work with Mach3, The usb to serial should work but they can be fussy, V6 has a setting for the COM port and XP uses emulation to drive the COM port, if you go to Mach3 software you probably don,t need to write any new software the on board software only contols the spindles and safety switches all step motors are controlled through the parallel port if there's a problem with the stepper drive this will probably be hard ware. To initialise the Duet you send Duet.dat which is a program for the 8032 so if you wished to program the 8032 it is just a matter of changing the Duet.dat .The serial cable used is a NULL modem cable, try sending Duet.dat via Terminal 9200 8 bits 1 stop no parity two LED's should flash as it downloads. I haven't much time at the momment but will reply when I can.
PS which version of Duet do you have 1 or 2?