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I fought the same issues for quite some time. FWIW my problem ended up being poor and dirty connections and poor grounding to the frame. I blew through two reg/recs and two batteries before I finally checked the simple stuff. Ended up replacing alot of bad wiring and such from the stator to the reg/rec to the battery to ground to correct the bouncing battery voltage when running. I hope I have it resolved. Best regards.

Found this year old aged thread that looks to be close to my situation on my KZ650.  The bike over the last few years seemed to progress on running down batteries even when new and fully charged.  This manifests itself when riding after a few miles.  The engine stumbles and slows as if I am running low on fuel.  Then it dies completely.  There is no sign of any current and no fuses blown.  To this point in my motorcycle maintenance/repair/rebuild career, I have avoided working much on electrical issues.  I do have a basic pocket size Craftsman voltmeter.  I am guessing I have a bad voltage regulator.  Do these regulators have the ability to degrade over time?  Thinking about the rectifier too.  Am I just taking stabs at this?  Is there a good place to start?  I am tired of going for a ride and needing to call a friend or the Mrs. to come and get me with the truck & trailer.  Any sources for voltage regulators, stators and/or rectifiers?  Please help here.   

The factory service manual has the testing procedures in it. If it were me, I would start with battery and work my way back to the alternator.

Fire the bike up.

Meter on DC V
Leave everything connected for all tests.
You'll have to backprobe connectors.

Black probe on neg battery post(metal part of battery
Red probe on pos battery post
Note voltage
Should be around 13 volts

Turn on high beam
Note voltage
Should drop but go back up to 13v

Raise rpm up to 2000
Note voltage
Should increase above 13v

Raise rpm up to 4000
Note voltage
Should be close to 14v

Thank you gentlemen.  Will give those a try.  BTW, I have the KZ service manual.  Other than a converting to solid state from points/condenser and new fuse box, the electrical system is original.