OK I have the spoken to the CAA and have the answer.
If you have completed the old syllabus 7 exams in their entirety before 17th September 2012, then you proceed to apply for the PPL using the NEW form NOT THE OLD JAR ONE, and you simply leave blank the exams field which are not needed, i.e. 'Operational Procedures' and 'Aircraft general Knowledge' which were part of the old Air Law and Principles of Flight.
Hope this helps anyone else trying to wrestle with the website....