Wow, that sounds like an awesome trip! Post pics, okay?

I'm not surprised that running is more fatiguing than cycling. I experience the same thing. Are you building in some rest days?

I guess it depends what your goal is when you run. Is it to be a better runner, or is it to cross-train so that you can be a better cyclist? If it's the latter, then I don't see anything wrong with only running a couple of times a week, just to mix things up a little and use some different muscle groups.

(And I totally agree with everything that Bike Chick says too!)