Cheers for the feedback, its not a diesel, its the 1.4 TFSI. I have had a second opinion and it is unfortunately what the first garage said. Its either an engine rebuild to replace the cylinders or a replacement engine im afraid.
It was very juddery on tick over and in the low rev range, and started throwing black smoke out the back (its burning oil).
They changed all the coil packs and spark plugs (one was absolutely black which was the one from the second cylinder which is scored) but it didnt stop the juddering or black smoke.
The final analysis was that cylinder 2 and 3 are