Config Done Fails to Go high with simple SOF file(Jtag+USB Blaster)

as your are using EPCS64 and not a manufacture other than altera the system should know the ID, so no overide file needed here

the thing with the id could be that it always reads 1 or 0

if your schematic is a mentioned in altera doc, have you tried to download a dummy nios design via jtag ? just nios + epcs controller and on chip mem to satisfy sopc. this dummy design is only used to be downloaded via jtag to give a running nios cpu and then via command line you can try to reach the epcs via nios and hopefully programm it.

the command line also gives some debug infos.

if the epcs always gives 0 or 1 then recheck all signals. try to monitor the epcs via scope to see if it respons (understands the commands)