My poultry barn was built in 1915. For the 10 years previous to our purchasing this place the previous owners used it as a catch all junk building (you wouldn't believe the garbage and filth, yuck) as well as left the doors open so that their mishap poor creatures of the goat, sheep, and pony variety wandered in and out at will. When we purchased the farm we required that the buildings be totally emptied. We didn't want to have to haul their junk to the dump. And so they did clean them out. But they didn't 'clean' them in other other way shape or form.
When we finally got around to having the energy to even think about any type of livestock we had to do some major cleaning. We had to shovel out tons of decade old poop from goats and sheep. We used a pressure washer and cleaned every room top to bottom making sure all poop(or as much as humanly possible) and other stuff was powered away. We used a standard disinfectant cleaner.
After the rooms where clean, we left them open exposed to clean air and lots of sunshine. We mixed a heavy strength mix of bleach and water and used a pressure sprayer to soak down every inch of the walls, floors, roosts, nest boxes, feeders, etc. We then let that dry leaving the barn doors open so that good ventilation and sunshine helped to air it out.
It was a good several weeks after that we began to build a layer of deep litter on the floors and a very good dusting of food grade DE. About 2 weeks later we moved the first of our young poultry stock into their new home.
We haven't had any problems with anyone being sick with illness or disease.
We are very sure we killed whatever germs could have been laying in wait under all of the poop for so long a time. While I am thinking about it you might want to get a few of those face masks to wear when cleaning out that barn incase of any air born illness that you could easily inhale and cause a respiratory infection in yourself.
Good luck. I have been where you are and know the job you are facing. I'll send good vibes your way.