Oh poor little Tatum, poor you, poor hubby and I'm sure Stedman doesn't understand what is going on either.
I would be irritated if my vet missed a baby tooth during a spay too. Try to think positive about her trachea since there isn't an "official" problem yet...I don't know anything about collapsed trachea other than the obvious use a harness never a collar, try not to let them get super excited, etc. but I'm sure someone out there will have some great ideas.
Hopefully, the Clavamox will help clear up her chest infection quickly, so at least you will be done with that part of the puzzle.
Sweet little Tatum has had a rough year to say the least.
I'll keep you all in my thoughts and prayers.