Thanks so much for the link. After reading what has been learned from so much experience, I feel more confident now continuing on with trying the deep litter method.
I added a lot more wood chips and I'm leaving the nesting area lid open a crack during the day and that seems to have solved the ammonia problem. I think I'll add even more wood chips.
I could probably use more ventilation too, but I'm hesitant to cut another hole in the coop. I understand that the chickens can withstand cold temperatures, but it can get really cold here some nights in the dead of winter, down to say -30F overnight.