Here's an old check from martinc:
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. In addition, the red-wire contact on the rectifier/regulator connector also has a history of oxidation/corrosion. Be sure to check these!
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 0.14~0.18 ohms @ 20C (68F). If not, replace the stator coil. Be sure to negate (subtract) lead resistance from your readings. To do this, touch the meter leads together and note the value of the resistance reading; subtract this value from your stator coil readings.
NOTE: Attempting to read around 0.5 ohms on an analog meter is difficult enough on the X1 scale, much less the X10.
I would like to add that when you check your stator resistance, also check each leg to ground to make sure none of the legs is grounded. You can also check the AC Voltage coming out of your stator. Unplug your stator and measure between legs 1 and 2. Then check 1 and 3 and then 2 and 3. You should have about 20 Volts at idle and around 70 Volts at 5k rpm. Also, the black wire on your regulator goes to ground. Check the resistance from the black wire to ground to make sure it's not open. Since your bike dies when the battery goes low, I think it's safe to assume your battery is good so you can ignore the instructions about checking the battery or installing a good one.
Mark