Can you post a picture of your rig? The first image that comes up when I do a search for "Toyota 21' Class C" is this:
Looking at this picture, the easy bits would be an undertray and skirts on the rear wheels. More complex might include somehow building a shell into the doors that would allow them to blend into the front of the motorhome body, more aerodynamic (or retractable) mirrors, flush-mounting the marker lights, and making the A/C retractable when traveling (or maybe making a more aerodynamic cover for it while underway.)
As far as the transmission goes, I know that in my Ranger, if I'm on the verge of the transmission downshifting out of overdrive, it's already unlocked the torque converter. If this is the case with you, you may actually get slightly better mileage in headwinds with the selector in 3rd (so the torque converter can re-lock.) A MPGuino or equivalent would definitely help you figure that out. And of course, I don't have to tell you that a manual swap would probably be a good (but expensive) idea.
Finally, you could probably have a small windmill or solar cells that you could use while stationary to charge the house batteries instead of charging them from the alternator while the vehicle is moving.