Nice write up, for sure. Thanks.
I also have a background in car audio. Back in the early 90's, I was an IASCA competitor and judge...took a car I built all the way to Nationals. Then, in betweeen a stint with GE, and my current job with a Corvette race team, I had my own shop for a while. Did quite a few clean cars, including one Car Audio magazine feature. I've done the loud (you do what people want to pay for), but clean and clear is my thing.
I'm toying around with a couple ideas for my 08 RG. Part of me wants to just ditch the head unit and speakers completely, and start over...maybe even a custom inner fairing, to take some 8's, or something. Another part of me says just upgrade the speakers, and don't add the extra hassle, expense, and potential for problems. I'll probably start simple, and end up getting into complicated before long. I've built many custom cars over the years, and most of the fun was in the build. When I finished, I usually sold them. With the RG, I so love riding, that I don't want the down time associated with the build...but I guess there is always winter.
Autobred, that Clean Sweep is certainly a fine piece, but I don't think I'd put it in a bike. Sure, you'll get a lot of 'improvement', but I just don't think it would be justified in the less than ideal environment of a bike. And it just adds one more component, which becomes one more potential for problems. Actually, I think the setup would be quite difficult, and you might end up with big problems. As you probably know, the Clean Sweep has a built in, basically non-user adjustable equalizer, designed to account for problems with factory systems (cabin design, speaker size limitations, head unit issues, etc.). I'm afraid that when you go to set it up, with its pink noise generator, that it will boost some frequencies excessively (bass, for example), which will just lead to trouble. That being said, let us know if you do it, anyway...

I don't have a ton of experience with them...I tried to avoid EQ's, if at all possible, and if one was required, I wanted one I could control. Now, some of the Rockford Fosgate stuff is interesting, like the 3Sixty products...at least you can see and control the settings.
My current line of thought is about boosting the mid range of the stock system. The low end is tough, without the modal reenforcement of some sort of cabin, and the high end is somewhat over rated. For one, most adults can't hear all that high any more, and more importantly, it just doesn't take much energy to reproduce those frequencies well.
I have a bunch of little 2" aluminum cone drivers I picked up for $2 each from Parts Express earlier this year. They look a lot like those 'bowl' drivers you see in ipod docks and computer speakers. Being aluminum, with rubber surrounds, they should be completely fine in the 'outdoors', and while the will lack much impact below about 200hz, they should have tons of midrange. They are 8 ohm, so I'm thinking about putting 4 on each side of the inner, using some version of the factory grill. They look pretty cool, and sort of match the gauge faces, so I might install them in some way they would be visible...like maybe black aluminum bezels, where the grills are now. I also might throw in a little hard dome tweeter, running from like 6khz up, just for good measure.
The plan is to mock something like this up later this week, and see how it sounds. I'll let you all know.
Toby