Somewhere in the past month I biked from 500 ft in Ithaca to well over 7000 here in the southern Rockies - I'm now at altitude and will be for the next week and a half. I worried about acclimating to the elevation change, but the only effect I have noticed is some muscle cramping. Of course, high altitude can probably just get lumped in with wind, hills, and heat. I can lose water easily up here too, without even sweating that much. The air is thin and the sun intense. With all this said, it's probably a good idea to take an off day here, and scale back the mileage for a bit thereafter.
Santa Fe is absolutely beautiful and contrasts a lot with the plains I was staring at the past week. I'll take some photos tomorrow during my day off.