12.5V does not indicate a flat battery, you need to do a load test. Lights on, engine off and see how long the voltage remains above 11 volts. Do not discharge below this voltage. I also suggest you recheck the stator resistance and output voltage readings, there may still be a poor connection. And finally recheck the battery voltage while the engine is running.

I'll try this when i get out of work. Cheers

Would the battery not charging on a charger not indicate a dodgy battery?

Bike chargers are slow chargers, can take hours to bring a battery to full charge depending on the state of the battery. Dud batteries are usually quick to charge because they offer little load to the charger and reach charger cut-off voltage quickly, although the opposite is also possible, which is why a load test after a full charge is the best way to determine the condition of the battery.

Cheers, Is there anyway to do a load test myself? Is it just seeing how the battery voltage drops when something such as the headlights are running, without the engine being on?

Yes, but do not let the voltage drop below 11 volts.

Thanks for the advice. Been bored at work today, thinking about my bike, so I decided to make myself a wee dash mounted Voltmeter. Hopefully aid me in my fault finding quest! Pics to follow!

Thanks again for the help!

Did you solve the problem? I think I have got the same problem

Yes I did. New battery seems to have done the trick. Did all the tests from electrex world. Doesn't take that long to run over all the checks with a multi meter. Also check the condition of the wires running from the stator to the RR.