I know its a little late, but being another person of altitude, I thought I would chime in.
The USDA has some cooking tips for us oxygen deprived folks.
http://www.fsis.usda.gov/factsheets/high_altitude_cooking_and_food_safety/index.asp
Second I would like to ask if the water pan was in place when you checked the MES 40 chamber temps. Don't laugh just yet, but even empty, I have noticed a HUGE difference in the way it reads temps, The heating element is exposed in the bottom right side of the oven. The chamber heat probe is directly above it. When the water pan is in place, hot air from the element goes directly to the thermostat, and turns off the heat. Even though the heat is cycling and reading at 225 the center of the smoker may be as much as 20-40 degrees cooler. Heat does not rise, Hot air does. The only source of fresh air is right above the heat source from the chip tray. Again directed by the pan to the probe.
Masterbuilt recommends that the pan always be in place when cooking so I will not recommend otherwise, instead look at the simple mod that Bear did to his MES40 to direct the heat to the center of the chamber. Look past the gorgeous bacon, you will see it.
http://assets.smokingmeatforums.com/f/f9/1000x500px-LL-f9f26196_DSC02348.JPG My deflector is under the pan, but results are the same.
Also, to cold smoke with the
AMNPS, I needed to add about a 2ft chunk of stove pipe to the vent hole (working as a chimney) to get enough "draw" of fresh air to keep it consistently lit. But my air is a bit thinner than yours.
Hope this helps and good luck.