Charging System Testing Made Simple
Charging problems aren't always the regulator, they can be caused by something as simple as a shorted wire. It's pretty easy to test, despite the directions in the service manual.
The alternator depends on the battery providing current through a field coil to produce a magnetic field. One end of the coil is connected through the ignition switch to the battery and the other end goes to the regulator, which acts as a variable resistor between the end of the coil and ground. The resistor, a power transistor, goes to its lowest value to allow the most current to flow and produce the most output when at idle or with heavy loads. When less output is needed, like when the revs are higher, the resistance is higher, allowing less current flow through the field coil. If the end of the coil is grounded by a short it will cause the alternator to produce full output all the time.
Use a digital voltmeter and measure battery voltage. It should be about 12.5 volts and drop to about 12.0 with the switch on. Start the bike, but keep the revs low and don't go over 2000 RPM. As you rev up the engine the voltage should increase until it's about 14.0-14.5 volts at 2000 RPM. If you rev it up a bit more, the voltage should stay the same and go no higher. If it still keeps going up the regulator is bad or the end of the field coil is shorted to ground. (Don't go any higher than 15-16 volts because you don't want to cause anymore damage.) Unplug the connector to the field and measure from each pin to ground to make sure neither is shorted. If that's OK then replace the regulator.
If the voltage stays at 12.0 volts and doesn't go up when the engine is revved up, then either the regulator or the alternator can be bad. Measure the coil resistances with the digital meter to see if they are in spec. and if not, replace the alternator. If the coils test OK, try grounding the non battery end of the field coil with a jumper clip, start the bike and see if the voltage goes up when you rev up the engine. It should go up as speed increases until you reach 14.5 volts at 2000 RPM. Stop there because the alternator is good and the regulator is bad or the wiring is broken or has burned up connections somewhere.
http://www.yamaha-triples.org/workshop/chargetest.asp?subheadingid=5&mainheadingid=1