Can you post any photos of your coop, especially along the top of it?
The way to control ammonia/ improve ventilation is to have lots of openings up at the top, where the ammonia rises, so that it can escape.
As an example, a recent post mentioned that the walls on all four sides of their coop ended 6” from the top (gaps covered with hardware cloth). No openings lower down allowed drafts to blow on the birds; everything was high over their heads.
That’s the level of ventilation needed, not two or three dinky holes drilled in the sides, as pre-fabs often have.