Well, from the above post, you might be able to gather, tonight, has been loom night.
Please take note, I had NO idea what I was doing, even with the most thorough diagrams available. This is real headache stuff. Luckily the wiring demigod that is Mr Trigg from VW was at hand to show off his skills.
By the end of it, I actually had a pretty good idea what was going on, every engine plug has been labelled, no matter how obvious it is, every wire from the ECU has been labelled and virtually all the wires that are to be run inside the car have got what type of connection they will need, also what amp they are to be fused.
This is an absolutely monumental step in getting this thing finished, really can't thank Mike enough for his help.
All the wires coming inside will have to be extended towards the fuse box, but with everything labelled up correctly and checked, should make things pretty easy. I'm 90% sure that we can put CE2 plugs on the end of most things to now make this fully plug and play which will help immensely if the worst ever does happen when this finally reaches the road/track and everything needs to be reshelled.
This is how it is now, I'd say over 85% of the wiring I had was unused, this, is a good thing!
Full OEM setup, working diagnostics port and every sensor catered for and working.

Shame I've got work tomorrow, else I would be getting very, very drunk!