With a lot of help from Mr wasa I setup a quick test to check if the key I had was matched to the ECU as they were from a scrap yard.
This shows how easy the PATS thing is to use and really nothing to worry about, there are even a couple of wires connected there that are not needed.
big_wasa was able to give me all the information needed to get it going even though he had never used a focus 60 pin EEC-V ECU.
And yes that is a 12v drill battery, I did also try a 9v but it didn't like that.
The info below is all from big_wasa
The ecu switches the earths. So with the led you connect the live to the battery via a fuse and the the ecu switches the earth.
There are four earths, one perm live and two switched lives. Two for the transceiver and one for the led.