Regardless of if bikes should have stereo’s, the problem your going to have is the current drain on the fxr's electrics. The battery will be ok for a short time (minutes) unless you plan to use low volume. The amp your looking at will draw around 8 - 12 amps so you'll end up overloading the bikes generator and probably will burn out the rectifier. (Read breakdown)
Still, if you don't running any lighting and don't indicate, and run the bike at full RPM it should be ok for a while.
Other things to consider.
The Amp’s Heat sink needs to be exposed to the air otherwise it will overheat if wrapped up for water proofing, maybe stick it under the seat.
Wire the power to the AMP directly to the battery via a relay (otherwise amp will discharge battery.
Use wire rated at 15 amps or greater for positive and negative feeds.
Make sure the speakers aren't paper based, polyprope door speakers are the way to go, the are designed with some tolerance to water.
The touring bikes with stereo's general have car size alternators and descent sized batteries and lower power outputs, hence are often used to annoy other rally goers until wee hours of the morning.
Personally, if you want good sound on a bike, get your self an Ipod nano, that way you can have loud music in your ears without subjecting your music to everyone else around you.

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