Hey Scott..sounds like you need to check the charging system.
I would start with the battery, water level ok? Next the cable connections to the battery, remove and shine up all 4 ends and the spot they terminate to.
Replace and snug them up good.
Still a problem?, put your volt meter accross the battery leads and note the voltage not running. 13.5v? You're good, lower not good, needs a charge. Start and note the voltage as you rev up the engine..does it go up? If the volts don't rise and you have water and clean connections your charging system may be in trouble.
Let us know what you find and we'll go from there.
If you need some hands on, let me know, I'm near Mayer.
Spring Valley AZ
'03 KLR 650/DS sidecar