I've never dug into a KLR charge system, but I had to trouble shoot my Suzuki Cavalcade and my Honda NX250's systems.
If the Clymer manual has instructions in it's trouble shooting section, try to follow that.
If you have a multimeter, use it both to measure voltages at different points as per the manual, and ohm / continuity as per the manual.
The stator wires can be ohm'd out and the regulator can be measured for output as well by measuring voltage at different points in the chargeing system.
Sounds like there is a problem in the generation of voltage from your readings.
You should measure, at the battery, at least 13 - 14 volts while the bike is running at least 2,000 rpm.
If you have accessories wired, You may want to disconnect them to see if any are causing shorts.
Also check for possible shorts in your wiring harness.
2017 Yamaha XT250
1990 Honda NX250 (Green/White)
2011 Kawasaki KLR 650 (Orange & White )
My KLR Page..http://www.powers31.info/2011_KLR650.htm
Mod's to KLR:
Power socket, L.E.D. Battery Indicator, Camera bag holder
Custom Saddlebag frames .
Louder horns, Firstgear Onyx tail bag.
Custom Aluminum Skid Plate.
Cut down seat with Custom pad.
Go Pro Camera mount.
Last edited by larry31; 09-01-2012 at 06:10 PM.