Phil,
I had a similar issue and wrote up the result here:
http://foc-u.co.uk/index.php/topic,4820.msg41194.html#msg41194As others have said make a range of measurements at different revs, also remember that battery voltages are affected by the cold weather so you will see lower voltages in the winter. The workshop manual voltages are for 20 degrees ambient temperature.
Our bikes are getting old now.
If the thought of adding wires is a little off putting, then it would be well worth while to clean up the wiring connector blocks.
If you measure the voltage at the Regulator / Rectifier and you are getting a nice 13 - 14V then you know there is a drop due to the wiring.
Hope this helps !
( BTW: I've not had a single battery issue since i made the mod, and i use the bike all year round (with heated grips and waistcoat in the winter) and i do quite short journeys ~5 miles to work, so not a great run to charge up the battery)