I often ride to mountain high restaurants. One at Ponderosa, CA is at 7,200 feet; other at Alta Sierra, CA is around 5,500 feet. No problemo with either with regards to idle (I'm on the old software).
Maybe you got a bad tank of gas or a plugged injector? I ran a bottle of water treatment cleaner through my RT once when it wouldn't idle. It occurred the day after I got a tank of watered-down gas at a Chevron station in Morro Bay. Bike idled like crap and I abandoned the ride that day for fear it wouldn't run. I ran a bottle of treament through it and it got better along with a new tank of gas. The mechanic at that time (when I had a local dealer) said that water-related problems occur the day after purchase when the water settles to the bottom of the tank and then gets picked up.
The really odd part was the purple-colored gel all over the fuel pickup sock in the tank when I changed the filter out months later. Don't know what that stuff was, but it also had a lot of sand in it as well.