When one of my chicks died, very possibly of Marek's Disease, I contacted a veterinarian at Cornell University and we discussed disinfectants.
I ended up using Virkon-S, a disinfectant that covers a lot of organisms.
It was in tablet form and I used two tablets per quart of water in a spray bottle. Very easy to use. Clean the structure with soap and water first, then spray with the Virkon-S and let sit for at least ten minutes or until it dries. I then wiped the coop down with clear water and let it dry again. No wait time to put the chickens back in after it dried. Opened everything up and let it air out, too.
It is recommended that you wear gloves, a good mask (N95 mask, available at Lowe's or Home Depot in the paint department), long sleeves and long pants when you spray. I have a smaller coop so I used a spray bottle but you could use a pressure sprayer for larger applications. I went a little nuts as I also had two brooders and all that equipment to disinfect too---my driveway looked like I was having a yard sale because I had everything spread out to dry in the sun.
Virkon-S can be ordered from Amazon. I got the pack of 50 tablets, 5 grams per tablet. There are places that sell it a bit cheaper but I needed it fast so I went with Amazon.
BTW, Virkon S eventually degrades to a non-toxic substance.
http://www.dolittlefarm.com.au/docs/VirkonBrochure.pdf
Also---can you post a pic of your shed?
There are some people here who are amazing at coming up with helpful suggestions for adapting sheds, building new ones, and improving existing coops.