I would appreciate feedback on the design of my coop/run remodel

I'm in the middle of remodeling my coop and I would appreciate input on what I have laid out so far.

There would be double doors to the coop (not shown) for easier clean out access.
Three nesting boxes with access from outside.
Three 6' roosting bars (and more will be in the run).
The area underneath could be storage OR a separate brooding area for hen and chicks. If used as a brooder, there would be a separate "zone" in the run for hen and chicks.
Door to run would be double width for wheel barrow, also a split/dutch door.

Anti-predator measures (not shown) in these images.

First and foremost, love the images! Super handy for conceptualizing the space.

Take the following comments/questions with a grain of salt. I built a coop and attached run once and just am trying to pick your brain in case you might of not considered some things like I did.

1. Is there going to be a roof overtop any of the run? (I installed a run with only wire mesh to protect the girls and in the winter/inclimate weather they were staying in the coop. I have made about four foot from the coop now covered and the girls are out much more with the overhead protection from rain)

2. Any interest in deep litter? One of my hindsight discoveries is that I should of made the chicken door cutout a bit higher. Mine is low and the girls kick out bedding near the door when it gets to a certain height. Its okay and still works, but I would of made the floor deeper.

3. Personally, I made the space underneath my coop open for the girls to flock under due to not having a run roof. I also pop their water/food under there to give it some protection from the elements.

Timothy Norton wrote:First and foremost, love the images! Super handy for conceptualizing the space.

1. Is there going to be a roof overtop any of the run?

2. Any interest in deep litter? One of my hindsight discoveries is that I should of made the chicken door cutout a bit higher.

We are on the same wave length!

Yeah, I've decided to clear tarp the roof of the entire run.
...and yep, I also do a deep liter in the winter.

I haven't decided on the final location for food and water.

In my experience, the most important single thing for a healthy coop is proper ventilation.  Yours looks to have only that small window for ventilation.  I made the mistake of not having enough with my first coop and my chickens suffered for it.  They got frost bite and a couple had respiratory problems.  That was all before I read Fresh Air Poultry Houses.  It was written in the 1920's and is the best book I have ever read on the subject.  It talks about the importance of ventilation, not matter the temperature.  In my new coop, designed after the book, my birds thrived in a coop with an open front throughout the winter, including two nights in a row of -40F.  They had no frostbite and no health issues.  The coop is uninsulated, and as I said, the entire front is open the entire winter.  The roost area though, is completely sealed and free of drafts.  I would urge strongly that you provide as close as possible 1 sq ft of ventilation per bird.  

Brody from this forum built the same style coop I did.  I don't have pictures of mine, but his is a beautiful example.  Brody's excellent coop build  This isn't to say you have to build your coop this style, allow it is a style I highly recommend, it is just an example of the amount of ventilation these coops have.  You can get the book free here:  Open Air Poultry Houses

The book also discusses deep litter, and as Timothy said, I think it's very worthwhile.  Also like Timothy, I made my door too low in one of my coops, and they constantly kick things out.  It doesn't matter because it all turns into soil anyway, but it's easier if they don't kick it out.