For your sake to save you a hea ache I hope it's the immobilizer because of the key the amount of effort you put into it yourself is unbelievable you deserve a simple.break
Nice one mate, yep it would be nice if it that simple but ive learnt with this car its never that simple, it always finds some way to bite you in the a**e! Lol.
Is it flashing immobiliser activated on the dash?
Happened to my project today and I left it charging with the ignition on for an hour and it stopped flashing and let me start it!
Just something you could try 
To be honest I can't remember but if I finish early enough today ill get over there and will try that out, cheers.
Looking to get vagcom off egay so once I do will be able to sort it out.