As this issue was niggling me, I decided to get it out of the way.
I found the VIN plate, loose inside the tool compartment under the bonnet. Comparing the documents, I see that the registration document had erroneously substituted '0' for 'D' and the MoT certificate had omitted a '0' altogether. I have sent photocopies of the documents, and plate, back with the required form to DVLA. Just have to securely mount the plate with pop rivets replacing the original adhesive.
Still find it puzzling that, after all these years, it has only just been spotted.