JT, you are correct, the higher you go, the richer the bike gets.
As you stated, the higher you go, the less air. You're looking for the best air/fuel mixture. So, if there's less air, you also need less gas to keep the air/fuel ratio the same. You will be loosing horsepower, but you won't get the strange throttle response. How does one not loose horsepower? Put on a turbo or supercharger, something that can shove more air into the engine.
What does this mean for you: Shimming the carbs means more fuel, richening up the mixture, which is the opposite of where you want to go. If you plan to spend a lot of time at elevation, you actually want to lean the carbs out, maybe half a jet size or a jet size, on the main jet. You might be able to get away with enrichening (backing out) your air/fuel mixture screw, which affects your "just-off", or "just past" idle stage, but I doubt it.
Here in CO I run my bike quite a bit on the lean side in the summer because I too like to play in the mountains. At my house (5,000ft) the bike is lean and hot. At 8,000ft she pulls beautifully, with a spot-on mixture, and at 10,000ft she stutters a bit, being quite rich by now.
In the winter I tend to run a bit on the rich side. On a nice warm day here in CO (40-50F) the bike is a little rich and pops in the exhaust, but in the morning and evening when I commute (10-30F), she runs like a raped ape, with a spot-on mixture. Nevermind the frozen fingers...
I don't need to worry about elevation changes in the winter because there's too much sand, snow and even colder temperatures in the mountains, so I don't go there. You would be surprised what 20F can do the air/fuel of your bike....
I have modified my air box, but my exhaust is still stock (can you believe it, even after 20K miles?). I run 102 main jets in the winter, and 100 in the summer. My idle jet stays the same year round, it's a 39.5 (made with drill bits). My air/fuel mixture screw is 2.0 turns out in the winter, and 1.25 turns out in the summer.
Shoot me back some questions....
