If its a MS-I V3 (pcb) then the bottom left of the board is a patch area for various options like 'shift light'. I've also seen it used for the second spark driver instead of mounting on the main heat sink !!

The only easy way to test the ECU configuration is a Stimulator, preferably the Jim Stimulator. Once you know the hardware and software are correct, then move on to the actual Zetec installation.

Martin