Just though id put a post on in case anyone else has this issue.
So the immobiliser had got wet at some point which had caused pretty severe corrosion on the plugs side of the immobiliser board.
If the immobiliser is completely dead there seems to be 2 options, you can either replace the ECU, immobiliser and key chips with one from a different GTi, the other option is sending the ECU to someone who can decode the immobiliser off the ECU.
I opted for the immobiliser removal option so i sent it to VAGTRONICS in Stoke, who decoded it very quickly and got it sent back same day!
Car now works perfectly!
Thanks for all the help!