Cold and damp may increase the smell. Nothing wrong with putting a fan out there temporarily to dry things out. Then you would have a better idea of where to go from there.
I should have also mentioned that part, maybe a big part, of why I am such a fan of using wood chips is that I can get all I want for free from our county landfill. Nothing better than free bedding. Plus, after I clean out the wood chips in the coop, I spread them out in the chicken run and let them compost in place. When I need compost for the garden in the fall, I will sift out shovels full of chicken compost. I built a cement mixer compost sifter just to harvest all that chicken compost.
Speaking of which, if you have dug out the smelly soil in the coop, you could probably mix that in a compost pile if you have one started. If you don't have a compost pile yet, I would suggest planning on it because chickens are natural composters. They scratch and peck things into compost in no time. You just have to let the chicken poo in the compost age for a number of months before use. Chickens and gardens go together well.

At any rate, you certainly have a nice setup there to work with and your planned improvements should make it even better.