I've never attempted to set up EFILive on Linux, but you may need to use linux drivers underneath wine to allow wine to see the ftdi USB devices. (http://www.ftdichip.com/FTDrivers.htm)
If you do, you may need to modify the linux drivers supplied by ftdi to use the correct VID and PID for EFIlive's devices.

VID=0403 PID=E4A0 for EFILive FlashScan FSP (i.e. V1)
VID=0403 PID=E4A1 for EFILive FlashScan V2
VID=0403 PID=E4A3 for EFILive AutoCal V2

Regards
Paul