So it seems that FTDI cable is broken for some reason. There should be no way to kill it if its connected correctly to drive SPI connector since it drives only optoisolators. Also nothing should be plugged to CMD connector same time since it shares pins (whatever is connected to CMD could potentially kill the cable). If cable still fails, it must be quality issue of FTDI. If this kind of issues start occurring too much, I must develop an alternative to that cable. Luckily it's not critical part for production machines as it is needed only for one time when setting parameters.
If you wish to try the improved Rev 2 (160V) drives, just email me and we could arrange you a chance to try it.
BTW, could you also list the other sharp ends and little problems you have encountered? That info would be used to iron them out