In regard to lack of charge:
1) Charge the battery overnight (7~12 hours), not to exceed 24 hours. 
You may exceed 24 hours if you are using a ‘smart charger’.
2) Disconnect charger and allow battery to stand for 30 minutes. 
Check the battery voltage with a digital voltmeter. The voltage should be around 13.3~13.5. 
If the voltage is less than 12.5, replace the battery.
3) Install known good battery into bike and start engine. 
After warm-up, bring engine speed up to 5000 rpm and measure the battery voltage at the 
same time. The voltage should be about 14~14.5 volts. If the voltage is greater than 15, 
the problem is most likely the rectifier/regulator. If the voltage is less than 13.5, 
then it’s either the alternator (stator coil) or the rectifier/regulator, 
or possibly even both. 
3a) SIDE NOTE: A problem that seems to occur with the R1 rather frequently is 
the 3-terminal stator coil connection fails and the resultant heat from the I*R 
drop melts the connector. Be sure to check this!
4) To check the stator coil (alternator), measure the coil(s) resistance at the 
3-terminal connector with an ohmmeter. The resistance reading between each coil 
(three total), should be 0.45~0.55 ohms @ 20C (68F). If not, replace the stator coil.
4a) Before measuring coil resistance, touch the meter leads together and record the reading. 
When you then take the coil resistance readings, subtract the recorded lead resistance reading from them.

I know I was a little rough on you at the beginning, but my point here is these are $10,000 machines 
and should be treated as such. They don’t deserve a ‘guess and by golly’ approach 
to troubleshooting/maintenance.

Sam Farris.