While I like the concept of a bare earth floor for scratch, I fear that this will lead to problems down the road.

Chickens are not the cleanest critters, they have no bowel/bladder control they go when ever they need too. Chicken manure/urine is acidic in the concentrations you will see inside your coop that amount of acid will kill most bugs in the soil.

All of that straw may counter some soil damage from the manure, but I doubt you will have anything you want in their, you might actually be making a breeding ground for mites [link to www.backyardchickens.com]

Note the preventions: Prevention:
Prevention of mite and louse infestation is difficult. Early detection remains the best way to control these pests. Keeping the coops and bedding clean and fresh, periodic scrubbing of the coop and nesting boxes with soap and water, and regular inspecting of your flock to catch the problem before harm is done to the chickens.

Of course its a bit too late to turn back and build a floor, however you might want to seriously consider getting several bags of quick setting concrete and dump them on the floor (when dry) then sprinkle with a mist of water until soaked, but not flowing out the door. Let it harden and it will make a hard enough floor. I have had success with stucco mix large grit sand) and making a hard surface that doesn't have lots of peppels. .5 to .75 inches is more than enough. Spread out with a push broom or a iron rake (not a leave rake). Also consider drainage, so have the floor slope a little toward and out the door.

For all of that bare wood, I would strongly suggest sealing it with that roll on bed liner stuff to about 30 inches above the floor line. this will prevent muck and manure from sticking to the plywood which will eventually eat through it. Above that an exterior grade paint should be enough to protect against condensation.

As for your nesting boxes, I strongly suggest you cut up the pieces of wood and cover them in the bed-liner stuff. Walmart sells it far cheaper than you would get at Napa or auto zone. After being painted' assemble your coop with brass screws, touch up over the screw heads with bed liner.

It is a plastic coating, it becomes hard and tough, and if you use a smooth foam roller it is real easy to clean. however it cleans up real easy, all you will really need is a hose and spray water to get most of the gunk out of the box.

Either have the front of your nesting box easy to remove to wash out the box, or make it to where stuff can flow through the back.

A lot of people make the mistake of using a wire bottom on their nesting boxes thinking it will be easy to clean... its not.

Your perch rails should be relatively easy to remove and replace. While you could paint them with bed liner, you would have to use a different applicator to make a rough surface to prevent the birds from slipping off.

That minor gap will be good for ventilation during the cold season and spring and fall, in summer you are going to want to open up something more for air flow.

If at all possible, install a couple of windows, either buy off the shelf and use chicken wire to replace the screen, or you can make your own with butt jointed frames and sheets of plexi (the hard plastic that comes in sheets, about 1/4 inch thick).

In summer you are going to want air flow through the coop, it keeps down the stink and if you have hot muggy summer having the windows open (with chicken wire to keep the birds in and predators out) there will be sufficient airflow to keep the birds happy.