I did some more diagnosing & research into this and have found the following -
* When I back probe the 6 pin plug at the regulator and check the charging voltage on the white (+) and BK/Y (-), I get an additonal 0.5 - 0.8 volts than what is obtained at the battery terminals.
* After speaking an experienced bike mechanic, the regulator will cause the system voltage to drop when the battery is fully charged to prevent overvoltage.

I was a bit skeptical of this initially, but I have never drained a battery while riding or had an issue with not having enough battery power for extended cranking on a cold morning. Has anyone hardwired directly between the reg & battery to bypass the various wiring splices & 20A fuse?

 

I have an 07, so my voltages may not apply, if I knew what they were, but....

If it is running & staying charged, all is good.

If the battery is charged, the regulator will cut the amps/voltage, that is what it is suppose to do.
If you have a low battery, then the regulator lets more amps/voltage through, that is why it is called a regulator.

Generally new battery's may not be fully charged. If your stopping and starting the engine, the battery will quickly run out of juice. If the battery is dead after riding 4 hours with 4 starts, then something is wrong, otherwise quite stopping so much!

 

If your voltage across battery terminals at idle is 13.3V and dropping with throttle applied, it seems almost certain that your voltage rectifier/regulator is shot.

First of all 13.3V at idle is too low, nominaly regulated voltage output (that's what charges your battery) is set to 14.4V. There is some voltage drop in your voltmeter leads, but you should be looking at 13.8V as minimum, but most importantly, this voltage must be constant at any speed.

The charging system takes 3-phase AC voltage from stator. This voltage however vary with the engine speed and of course is not suitable for the rest of the DC system.

Voltage rectifier converts it to DC, but this DC voltage must remain constant with speed (otherwise battery could be "overcooked" at high rpms) - that's where the regulator kicks in to keep voltage constant regardless of the engine speed. This voltage has to be also higher than nominal voltage of fully charged battery, otherwise the charging will be impossible.

 

Charging system specs from the '09 manual:

Charging voltage: 13.8 - 14.8V
Alternator output voltage (no load) 41V or more @ 4,000rpm
Stator coil resistance 0.3 - 1.0 ohms
Regulator/rectifier Resistance see text {I'm not typing all that,sorry}

End quote from manual

So as long as your charging voltage is over 13.8, you're OK. They don't say anything about rpm. It does seem a bit odd for voltage to drop with rpm increase but if it stays above the low limit, just ride.

Swing, first thing you should do is, properly, fully, charge the battery. Any running testing on a charging system call for a known (proven) good battery, freshly charged. Be careful what charger is used on an AGM (absorbed glass mat) battery (stock KLX). They need to be charged slowly. Car battery chargers, even most trickle, are too fast, they allow too high an amperage rate.

 

http://www.electrosport.com/media/pd...ng-diagram.pdf

The above free PDF from electrosport may be of some help in your troubleshooting procedure. I used it to isolate components while T/S'n my FZ1.
Also factor in ohms readings measured when the bike is cold and when it is warm (bike shut off). You may get a reading within limits cold but then fails after the part is warmed up. Parts can get expensive so it is best to do as much isolation as possible before ordering replacements. Don't forget to look at the simple things like a poor ground connection, electrical connections, chaffed wire, old battery etc.