After 4 weeks I finally received a letter from the DVLA. Thinking that this must be the letter I had been waiting for I quickly ripped open the envelope only to find bad news.... They were requesting that I:
a) Re-stamp the chassis and VIN Plate with a NEW VIN number issued by them. Not sure why, but arguing didn't help
b) Inform HMRC of the new VIN number (which they issued...!) via their NOVA system. NOVA stands for Notification of Vehicle Arrival, and is used to inform HMRC of cars coming to the UK from other countries! WHAT! I argued (politely), but they insisted this was the new process.
2 weeks later and a few nudging via again polite phone calls, I received my v5 document. PHEW!
The sun is shining and I have number plates and a big smile on my face!!
My advice to other builders would be to check with DVLA before you stamp the VIN number on your chassis and check whether a NOVA application is required. Get the NOVA application started at the same time as your DVLA application - it'll save 2 weeks.