Sorry for such a late response. This problem actually took two years to get mostly sorted.
What I did from June 2010 to the present.
-Got the diode box completely checked and re-soldered by a motorcycle electrical business. (didnt help)
-Brushes rechecked. (didnt help)
-Wiring checked, changed some connections to brass if i can remember correctly?
-Changed brake light to a smaller globe
-Initially changed regulator to a car regulator, then it was found that this wasnt working (faulty?) changed to BMW regulator this was found to be faulty (really?), then changed to another car regulator (cant remember what type but can check if someone is interested). This seemed to do it, the bike charges much better now.
-Replaced motorcycle battery with a full sized car battery (again i forget which type, but can check). The battery takes up all the space underneath the seat (no space for the little compartment thing that goes there).
-Fixed starter motor (bike does not struggle to start now, usually starts with one or two flicks unlike before. Means it drains the battery less at each start up).
Now im not convinced the bike is charging 100% of what it should, because the Generator light can still be seen dimly in the dark indicating a minor problem, but the bike works fine for me. It charges well in the day, charges at night with the lights on, and has no problem with doing lots of short trips in traffic (~5km).
The three main things that helped for me where
1) A regulator that seems to work properly
2) A larger battery
3) A fixed starter motor