Pics would help, if you can get some
I didn't want to put hardware cloth between each one on my shed coop, either. I actually have 2 coops, a duck house, and a goat house.
On the smallest coop I have, I just stretched hardware cloth over the entire top of the structure before putting on the rafters. But that won't work if your shed is already built.
For my ducks' house, I cut long strips of the hardware cloth and attached them inside the house snd over the vents. I cut slits where the rafters we're, pushed the hardware cloth between them, and attached it to the rafters themselves. I toyed with the idea of doing that on the outside and just bending it up into the the rafters, but it would've looked really bad, so I put it inside, which was a real PITA. Idk if that makes any sense.