Hi, David you need to perform the following tests:
1. Fill acid type batteries to proper levels.
2. Charge battery overnight at 1-2 amps you need 12.5 volts or better after charging and it must be able to pass a proper "LOAD" test you may have cursory readings of 12.5 volts or more but little or zero amperage the battery is faulty and must be replaced, AGM batteries have this issue more so than lead-acid types.
3. Check battery terminals for damage or corrosion, check the battery cables at "BOTH" ends for loose, corroded, or broken connectors, "INSIDE" and outside the cable harness, perform connector wiggle test and check cables with an ohmmeter if necessary.
4. Hook up battery positive cable, then with your multimeter on the milliamp scale connect one lead to the negative battery post and the other lead to the ground cable. The meter should read 3 milliamps or less, 10 milliamps with a radio, 15 milliamps with radio and CB. If your multimeter reads higher you need to isolate the circuit by pulling fuses and circuit breakers one at a time and observe multimeter for a drop in amperage then get out your test light and track down the short in that circuit.
5. Hook up the multimeter to the battery set it to DC volts and start the engine if multimeter falls below 9.0 volts while cranking you need to perform a proper load test on the battery and replace if necessary.
6. With the engine running at 3600 RPM, the battery should read 14.3-14.7 volts if not continue tests.
7. Unplug the voltage regulator from the alternator at crankcase by the front of the primary cover.
8. To test voltage regulator go to https://www.youtube.com/watch?v=F8EjV0IjW9Q
9. With the multimeter set to the ohms scale, with one lead grounded, touch an alternator pin ohmmeter should read infinity, if not replace the stator.
10. With both leads touching alternator pins, multimeter should read 0.1 to 0.2 ohms on 1989 and later models. 0.2 to 0.4 ohms 1988 and earlier models, if not replace the stator.
11. With the multimeter set on AC volts scale, both leads touching alternator pins multimeter should read 16 to 20 volts AC for every 1000 RPM'S 1989 and later and 19 to 26 volts AC for every 1000 RPM. If not replace the rotor.
12. Check for excessive wattage load from the headlight
For more information about your issue and valuable "FREE" downloads that you will need for viewing or printing please click on the blue links below. Good luck and have a wonderful day.
Kawasaki ER 5 Electrical Short Biker ie Forums
KAWASAKI ER 5 Service Manual
OEM Parts for Kawasaki