Wyatt, considering that you were living in N. Arizona at the time and based on what you describe with the eyes and breathing in particular, I'm almost certain that what you saw was a skinwalker (yenaldlooshi). The way that you describe it having "shimmering things" about its face is dead on for a skinwalker. Skinwalkers use pastes to add to their "masks" and these are both white and black. The white paint is not like the clown paint that one would immediately think of. It glows a little for whatever reason. This is why there are so many comparisons of skinwalkers and ghosts. I remember the one that I saw was a breathtaking white to the point where it seemed to glow in the darkness of the night. The white paste is just not the same as clown paint.
The sounds that skinwalkers make are also pretty much along the lines as you describe. They DO speak in Navajo but, for the most part, the noises they utter will be animal-like--grunts, whines, whimpers, growls and so on. They will scratch at windows and exterior walls and they definitely have a propensity for being peeping toms. There are so many accounts just like yours where something was outside, making some odd noises and looked in the window. Who knows why they like to do that. 99.9% of skinwalker activity is, however, non-aggressive but pure terror tactics. A good night for a skinwalker would be easily obtaining and planting whatever they need without being shot at or having any direct contact with their intended victim(s). That's not to say that they won't harm or kill anyone--they will if need be and are very capable of it.
A misconception that has cropped up on this thread is that skinwalkers will not go after non-natives. That is terribly wrong. A good 50% of the sightings that I have collected have been reports from non-natives. In fact, some of the more drawn out encounters have involved non-native families because they were unequipped to be confronted with a bit of Navajo mythos in the middle of the night. Skinwalkers will be very brazen with non-native families. The reason is quite simple: non-natives living out here are some of the easiest marks for skinwalkers. The difference between how a native family will react to skinwalkers and a non-native is huge. Most native families, if living in rural circumstances, would not hestitate to grab guns and start firing at skinwalkers. This is because the lore has it that it is perfectly okay to shoot a skinwalker. A skinwalker is so abominable in its actions that it has been stripped of its humanity by tribal view. Us non-natives, however, are going to be significantly less likely to be firing guns at something that we aren't even sure what it is. It's a difference between growing up with something and its lore and coming into an area to encounter the same thing with no prior knowledge. Skinwalkers are at a kind of war with people--both their own tribe, the surrounding tribes (the majority of tribes out here were long standing enemies of the Navajo) and with white and hispanic peoples. Most likely, from their viewpoint, we're all bad. The Navajo are bad for ousting them from the tribe. The Ute, Zuni and Acoma for long standing wars. The Hopi probably have it the worst because the fighting is still ongoing between the two tribes. Hispanic because of the history of the spanish in the area and european backgrounds--well, scorched earth and the long walk didn't happen THAT long ago... Skinwalkers are equal opportunity terrorists.
Burtontool,
Those are some pretty good skinwalker sightings. The speed thing always is interesting. They can't keep up great speeds for very long but they can long enough for somebody to get a good look at them. She probably wasn't running at 65 mph. Think about how it is when you pass a car that is going a few mph slower than you are. You don't pass them in a blink. It takes a few. If you had been going a little slower, I have no doubt that she could've kept up. There's a story that I was told by a Navajo man where he had the opposite experience, timewise. For him, it was dusk and he encountered a group of skinwalkers, running towards his truck at a V, on their way to wherever they were going that night. You encountered one going home. Kind of cool.

Alot of stories do have them rising up on their two legs to make it very clear that they are not an animal.
Deer are probably the first animals that skinwalkers sought to emulate. There's a Navajo story about how a hunter wanted to improve their hunting and thought to use the skin of a deer to dupe more deer. One of the Yei'bei'chii came down and helped teach this hunter how to perfectly emulate a deer. This was before skinwalking became so corrupt and perverted. It's almost ironic that skinwalkers most likely preserve some very old traditions of the Navajo.
Your uncle, considering his situation, probably had one heck of a time out here as a mormon missionary. Missionaries, from any creed, that opt to live out here can have some pretty wild encounters. One of my husband's favorite stories is about a Christian minister and his wife who came to live out in Fort Defiance. They were so terrorized by skinwalkers and so obstinate about offers of assistance from their parish, that they literally had one hovering over them while they slept. They left the reservation. It's unfortunate that people who come out here with the best of intentions sometimes become the target of such activities. It shouldn't deter people from coming out because this area does need help. They just need to be aware that they may have to seek assistance from medicine men in order to get things to stop. Skinwalkers are pretty prolific jumpers. I don't know about hundreds of feet but they can easily jump from the ground to a rooftop without much effort. They push off with both their hands and feet.
Cool thread and ty to whomever alerted me to it.