Hi Darrion
You can use both the Mondeo and Focus ECU's in principle but with one big exception - the Focus has PATS (Passive Anti Theft System).
Basically the Focus ECU relies on an input from a chip in the ignition key to allow the thing to work. I think you can get around it by taping the original ignition key to the ECU as it uses transmitter and reciever to identify the presense of the key.
The Mondeo ECU does not have this feature.
Other thing to mention is the speed input - I think the ECU will go into limp mode if the speed input does not match what it expects at a particular engine load etc. As this is picked up from the ABS hub on the front wheel this will need to be sorted.
A major difference between the Mondeo ECU's is that the manual car ECU has the EDIS module for controlling the coil pack integrated into the ECU. The Automatic version has a seperate EDIS module in the engine bay. Something else to consider as I'm running an ECU from a manual vehicle to avoid the extra components.
I'm about to use an OEM ECU and engine in my RS so i'm sure I'm up for a few hurdles but I cannot see why it wouldn't work.
Hope this helps.