Not been into chickens as long as many others but here is my two cents...
All chickens can fly except Silkies whose feathers won't allow them to get aloft...but that doesn't mean Silkies won't try to keep up with the other sorts of chickens they are raised with. My Silkies were raised with Welsummers and Easter Eggers and have always roosted with them on the highest roost and gone up and down the steep pop hole ramp. If you expect Silkies to "fly over" the low fence to get out into the yard they'll need a couple steps up to the top rail to get over. You'll need to create a ramp or step ladder idea for them inside the coop as well...bottom rail about a foot off the floor, second another foot up, etc.
Many folks prefer their highest roost to be about human chest high for ease of examining their chickens when they are roosting. That is when they are the most calm and easiest to pick up and look over for mites, etc. I've found that very helpful in training my chickens to allow me to examine them!
Consider you will need to clean both the roosts themselves and the area under the roost the most often as that is where the most poop will be deposited. Start a compost pile, barrel or bin and position it close enough to the coop for ease of cleaning.
Please remember that chicken wire will keep chickens in but isn't strong enough to keep any large or small predator out.
Ventilation and plenty of it is essential for any coop. The ability of fresh air to enter and exit taking the ammonia with it, with out creating a draft of air on the chickens while roosting, needs to be your #1 aim in retro-fitting your shed. Determine where the prevailing winds blow in your yard and vent accordingly. If it were me I'd put a couple of cupolas on the roof peak.
What a blessing your shed is...easy to convert, tons of room (remember chicken math!)...lucky, lucky you and your chickens!!