100 watts of extra lighting shouldn't be a problem for the 590 watt FJR alternator. That's only 7 amps or so. Heck, sitting at idle with the brakes and turn signals on is 80 watts or so. I'd be curious what the output on the red wire from the Regulator/Rectifier is, using a clamp-on DC ammeter (if available). The spec says the system should be capable of delivering 40 amps at 5,000 rpm.
Do you have access to an oscilloscope? Looking at the battery voltage while the bike is running and charging should show an AC waveform of regularly spaced positive-going crests forming a smooth ripple that increases with RPM. An irregular pattern is a sign of charging system trouble. For example, if every third crest is missing that suggests a blown regulator diode or failed winding. A negative going third crest suggests a shorted regulator diode.
A less accurate and reliable check can be done with an AC voltmeter, which can't show patterns but at least can measure the AC ripple. If the AC voltage is more than, say, 100mVAC, there's a problem.
A common problem with motorcycles in general is corroded connections between the alternator output and the rectifier/regulator input or between the regulator output and the battery. The FJR uses a permanent magnet 3-phase alternator system. Rather than vary the alternator output, this system runs the alternator at full output all the time and simply dumps excess current when the demand is less than the output.
There are 3 white wires going into the R/R from the alternator. The contacts should be clean and bare. Any corrosion on a contact will reduce output from that leg (and often results in partially melted plastic connector housing due to excess heat generated by the poor connection).
With the 3 white wires unplugged from the R/R and the engine off, set your resistance meter to the x1 ohms scale and measure the resistance between each pairing on the harness side. The resistance should be low -- around 0.5 ohms -- and equal. A high resistance indicates an open winding or broken wire.
With the red and black wires disconnected from the R/R, measure the resistance between the red and battery + then the black and battery -. It should be near 0 ohms in each case. High resistance suggests a poor connection somewhere.
With the engine running, measure the voltage between each pairing of the white wires on the harness side. The AC voltage between any two of the three should be equal to the voltage between each other pairing at any given rpm. IE: 1-2 = 2-3 = 3-1. (Seen on a scope, each pair should show a nice even sine wave.) Significantly lower voltage on any pair indicates a failed -- probably shorted -- winding in the alternator.
If everything else passes, replace the R/R.