it does somewhat, but the OP doesnt mention having a tune to begin with so with his mods he is already leaned out. if he does have a tune and forgot to mention it then it probably still needs a little update of he just has bad gas in the car

 

There's only so much compensation you can do for thin air. I have no idea how Goldenpony's car ran "fine" at the top of Pike's Peak. I can tell you my 06 GT with the brenspeed tune was falling flat on it's face when I took it over the top of the Cook City pass (10,000 ft). By flat on it's face I mean it was noticeably slower and had lost a significant amount of throttle response and power. Was it faster than my Honda still? Well sure..

But it was easily noticeable, the difference, between being at 3200' and 10000'.

 

What octane is your car tuned for, and what quality and octane was available in Vegas? I am convinced that we just don't get the same quality gasoline up here.....Even though the brand and octane ratings are the same. There are rumors of a couple of places in the metro area that have 93, but most of the readily available 91 is crap. Some may say that I'm smokin' those funny, left-handed cigarettes, but my car (stock with a 91 canned Predator tune) seems to be a little happier when I fill up at Shell.

Based on my experience tuning my other car (supercharged Tacoma with all kinds of goodies), I would venture that, if anything, you are running RICH, not lean. I am also willing to bet that whatever vendor wrote your tune file has turned off any adaptive learning feature....the part that would normally compensate for any slight changes in air density or fuel octane.

 

Disconnect battery for 20 minutes (negative cable only) and reattach.
Drive as per the owners manual to relearn the adaptive learning.
See if that dont match your mustang to the thin air enviroment.

 

drove the blue ridge parkway and around 6-8k feet could definitely feel the elevation sapping the power.

 

http://en.wikipedia.org/wiki/Beartooth_Highway

Drive that. I guarantee your car is gonna be "sucking wind".

Even the Subarus with the turbochargers I drove that road with could tell a difference.

 

Our engines suffer about 5 hp loss for every 1000 feet of elevation. Of course, weather and ambient temperature, as well as humidity all play into that as well. At our race track here in Billings, the air is the equivalent of 6700 feet of elevation, even though the track is at 3800 ft elevation. That number varies though, as the temp and humidity change, as well as the air pressure. Any way you cut it, the higher you go, the less power you have.

As far as your tune is concerned, there are a couple factors. First, as the air gets lighter (higher elevation) the MAF sensor will see this and compensate with less fuel, therefore your AF ratio will remain more or less the same. In a carburated engine, you will go richer as you go up in elevation. Second, higher elevations don't require as high of octane rating in the fuel, so where you probably got 93 octane in Las Vegas, you probably won't see higher than 91 in Denver. The reason is with less air, you can run lower octane and still not detonate because you run richer.. of course this is BS because our engines adjust for it, so we just get screwed on fuel quality. If you have a 93 octane tune, while it SHOULD be OK, you might be running just a little high (lean) on the AF ratio (from the tune, not the gas or elevation), and your computer might be pulling a little timing to keep it from detonating. If that is the case, for every degree it pulls, you lose about 5 hp.

You shouldn't be getting any codes just because of elevation change, I would suspect the tune or an o2 sensor failure, but it's tough to say..