Post Master General
Join Date: Apr 2012
Location: Bowling Green, VA
I Ride: '09 ZX6R
Sounds like the alternator is not putting out as much power as it should..... hard to say for sure, without knowing more about how old the battery is. If the battery is more than 5 years old, it is likely causing a lot of strain on the charging system, because it will not hold as much energy as it did when new.
If you have additional electronics on the bike, that will also cause the charging system to work harder than it is meant to.
You may have dirty or corroded electrical connections --those create resistance, which takes more power to overcome..... straining the charging system.
The diagnostics in the shop manual are pretty comprehensive, for troubleshooting the charging system.
The bike should be able to run, just off the battery for a time...... that means you can start the bike with the alternator disconnected from the regulator/rectifier, and measure the AC Volts coming out of it. Any pair of the three wires from the alternator, should have at LEAST 57 VAC (~ symbol) between them. 75 VAC between all three phases, is a really healthy '09 alternator. You should see maximum AC Voltage, with more than 3K RPM.
If you don't have even values between all three phases, odds are pretty good the alternator is damaged.
If that's okay, you have to move on to the DC side of things, which you have mostly already looked at. This is why I suspect an old battery, first. Pull it out and get it load tested. Replace if need be.
"Basic stuff fellas. Use your head for something other than to break your next fall."