I don’t know where you are in New Mexico or how hot it can get or how cold it can get when you see an extreme. Heat is a much greater risk for chickens wearing down coats year round so you are right to be concerned. That metal building is a concern too but if you put your nests and roosts on the more shaded north and east sides you can help that a bunch. Also, don’t crowd your roosts right up next to that metal roof. Give them a little separation from that hot roof. You probably are high enough the nights cool off reasonably but the metal can store and radiate heat.
It sounds like you have pretty good ventilation but it’s pretty impossible to have too much ventilation. In the hot part of the year that means below them when they are roosting and above them so the hot air that rises has a way to escape.
The roosts do need to be noticeably higher than the nests but it really doesn’t matter if the nests are 4” or 4’ off the floor as long as the roosts are higher. There are advantages and disadvantages to having them high or low but those are more for your convenience than the chickens. Pretty much the chickens don’t care but humans do. There are all kinds of nests too.
How’s your back? Do you have any problem bending over to gather eggs from a nest on the floor or is it better for your back if the nests are higher? If the nest you use is covered this may be more of an issue than with a nest that is open on top.
If your coop floor is dirty the chickens might scratch a lot of trash in the nests. If your coop floor is not dirty or the sides or lip is high enough, that is probably not an issue.
If the chickens can’t get under a nest and you have a solid floor in your nest instead of having it on the ground, that may make a great place for Mommy Mouse to raise a family. If chickens can get under the nest, well, they eat mice if they can catch them.
I’ve seen a broody hen get newly hatched chicks down from a 10’ high hayloft so this does not bother me nearly as much as it does some people, but some people really worry about a broody hatching chicks in a nest a bit off the ground. If you are not going to let a hen hatch chicks in there it’s obviously not a concern to you.
If your nest is more than a couple of feet off the floor, it’s probably a good idea to put some type of perch or landing place for the hen to use to get into the nest. For many chickens it is not absolutely necessary but it’s not a bad idea. If you have a chicken that cannot fly, like a Silkie, you may need to provide a ramp up there.
If the nests are pretty close to the floor, a hen may see the area under the nest as a good safe protected place to lay eggs. A fake egg like a golf ball in the real nest will really help with that but you are dealing with living animals. Nobody can guarantee what they will do, but we can give you some help in influencing what they are likely to do.
If the hens scratch out the nesting material, fake eggs, or even real eggs, you probably don’t have a high enough lip on the nest to keep that stuff in there.
There are a lot of other reasons you might want to put your nests high or low. We all do different things for different reasons. It’s not a case of one way being right and every other way being wrong. It’s whatever way works for you. The good thing is that the chickens pretty much don’t care. People do.
2x4’s are fine for roosts. It really doesn’t matter if the wide side is up or the narrow side, though you will get some people that are adamant their way is the right way and everything else is a disaster. If you do use sawn lumber if any type, I suggest you sand them. Part of that is to round off the corners so their feet can grip a bit better, even on the really wide boards, but my main concern is to avoid splinters. Personally I use tree branches. I find that they are just as likely to roost on the smaller ends as the wider ends even in cold weather though you will find people on this forum convinced that chickens cannot bend their toes to get a grip. I know I don’t really get cold temperatures. My lowest is usually just a little below zero Fahrenheit which is not that cold for chickens, but I have not had any problems with chickens’ feet freezing when they are roosting on the fairly small portions of the roosts.
Your chickens will do OK in that run without any vegetation in there. It will get muddy when it rains and I hope you do occasionally get some rain, but as long as it is positioned where it will drain and you don’t have it where rainwater flows into it either from a sloped roof or on the ground you should be fine.
Vegetation probably won’t grow in there. They will eat practically anything green then scratch up the roots and eat them. They will still enjoy dust bathing and just hanging out in the run. I do suggest you provide shade for them, not just overhead but in the south and west where the sun really beats in. Maybe leave the bottom open so the wind can get through. Part of my run is covered but it does not provide much shade. The sun mostly comes in from the sides, not from overhead.
How many can you keep in there? There is a big difference in what you can shoehorn in there and what I’d do. We keep them in so many different conditions, with different goals, different flock make-ups, in different climates, and use so many different management techniques there is no magic number than is the same for everyone regarding coop space, run space, roost space, brooder space, hen to rooster ratio or anything else. In general I find the more space I give them the fewer behavioral problems I see, the less hard I have to work, and the more flexibility I have to deal with problems.
I understand that if you don’t have the experience with chickens you don’t have anything to base the number on. There are various rules of thumb used on this forum that will keep most of us out of trouble most of the time in a wide range of conditions and management techniques. These are generally geared toward smaller flocks kept in suburban back yards. For a lot of people they are overkill though occasionally someone will get in trouble with them. The more chickens you have the less these rules of thumb mean. For example, one rule of thumb is 1 nest for every 4 hens. That works pretty well for a relatively small flock but if you have a lot of hens they really don’t need that many nests.
One rule of thumb often used on here for those small suburban backyard flocks is 4 square feet per chicken in the coop along with 10 square feet per chicken in the run. If you have a lot of chickens you can probably get by with less space but that depends some on how you manage them. You may wind up managing a lot of chicken poop too. Personally I like to give them more space for the reasons I mentioned above.
If you ever want a broody to raise chicks with the flock or you want to integrate new chickens that goes much better if you have more space. Just a couple of examples of the added flexibility you get with more space.
This is way too much tying I know but hopefully you can get something useful out of this. Good luck and welcome to the adventure.