The guys have pretty much covered lots of great information here.
As far as bass goes could be a few factors in that.
The box or sealed area can be a huge factor.
I would get the sealing compart that mounts behind the speaker if the fairing is not sealed.
I personally would go with the 6x9 for the lower frequency response and higher sensativity ratings.
If I could hear bass on an electra glide with subs, I'm not going to hear it out of two 6x9's no matter what I do. As long as it has clean mids and highs, and is loud enough to hear on the highway, I'm happy. I have a nice system at home and one in my car if I want really excellent quality music. I want a fairing on my bike for the looks and wind protection, and I prefer the look of these bigger fairings anyway, and the stereo is a nice plus for longer trips!
I'd be ECSTATIC if I could get decent bass, but, every bike I've ridden with a stereo, some with subs, some with aftermarket 6.5" speakers, etc. All of them the bass disappeared as you got up to speed, even though it was clean and there was plenty of it at a stop.
Running at full clean output (or put another way, running to the verge of clipping) an amp will average roughly 1/8 of its power output when playing music. Some genres and stuff that's heavily compressed can increase that duty cycle but it's a good all around number. This, coupled with that you're seldom going to be running the thing WFO, means there really isn't that much average power draw despite the amp's power rating.
You're better off to get a bigger amp and have clean power available than to undersize the amp and risk sending clipped power to the speakers. Not only does clipping sound bad but it can contribute to damaged speakers as well.
Okay so bottom line, the VN900 has roughly 6 amps of leftover alternator 'juice' per Kawasaki. (70 watts, 12 volts). I also have some extra tail lights on my tour pak (albeit LED), and I will probably convert my turn and tail to LED. So, with all of that in mind, do you still think an amp would be viable? Any suggestions on an amplifier?
Also would there be any realistic disadvantages to putting a 4 channel amp (if I went that route) in the tour pak? I could probably find a way to mount it in the fairing, but, the tour pak would be an easier mount. That would mean running the pre-amp lines under the tank back, and then the speakers wires back up to the fairing (and perhaps two more inside the tour pak to speaker pods, though I'm not 100% on whether or not I want to invest in speaker pods, definitely won't do it right away)
Alpine also has a 45W RMS x4 amp that is very small and wires inline with the stereo (using the stereos wiring harness for juice, and speaker level or RCA level inputs) so that's an option too for size.