Thought i'd update you all on our status as of today.
Thanks for the update and all those pictures. You really have a nice setup to upgrade. Most of us wish we had something like that to begin with.
I like the idea of some good primer to paint the inside of the coop. That should block the smell on the wood and lighten up the inside at the same time. If your dirt floor still smells, I'd take out a few inches more off the top. If you get to a point where you don't think you can remove anymore dirt, and the dirt still smells, I think I would try to cover it with some plastic sheeting to lock in the smell, and then put a good layer of sand on top of the plastic. If you have access to free wood chips, I really think they are the best for deep litter bedding. I would throw a nice 4-6 inches of wood chips on top of the sand.
In addition to getting free wood chips at our county landfill, I also have my own wood chippers at home. I got a few green branches from a pine tree I trimmed up and put them through my chipper. I added those pine and pine needle wood chips into the coop and it smelled like a pine forest for a short week. But then the pine smell wore off. Still, it was a nice air freshener. Normally, with a deep litter of wood chips, it should smell like a forest floor. I like that smell.
I have used sand before, but I found that it does not take long before it begins to smell pretty bad and needs to be cleaned out and replaced with clean sand. Sand does not absorb the smell. For me, keeping the sand clean and fresh was a lot of work. I live on a lake, and there is no shortage of sand, but I got tired of having to clean out the sand all the time. In my case, I think I got maybe one week before I had to clean it out and get fresh sand. With the wood chips, I only clean out the coop twice a year and it never smells. But wood chips works better for me where I live. I know other people prefer sand for where they live.
Anyway, love reading about the progress on your coop modifications and look forward to seeing more pictures in the future.