He may have cracked that tooth, he needs to see a pediatric dentist. That way you can rule out an injury. Sometimes they are deep inside too where we can't see the cracks or chips.
The temperature may also be causing him pain. Watch to see if the foods he is eating are all the same, maybe room temp, maybe barely warm, etc...if it's too hot or cool it can be painful to have in the mouth.
I would give him other drinks besides the milk. Is he still really on formula? or were you calling regular whole milk by the word formula?
I let all my grandchildren stay on the bottle for as long as the wanted it. I had no issues taking it away either. They just got tired of it and wanted other stuff. It does not hurt them in any way to drink fluids from a bottle.
Milk is milk is milk. It does not matter if it comes from a bottle, a cup, a glass, a pouch....
It does matter if they are holding that milk in their mouth all night while they are sleeping. The issue with milk rot is that those kids were keeping their bottle in their mouth all night and the saliva did not get a chance to rinse the milk out of the mouth.
So if you still have your child taking a bottle full time then just make sure he is not holding it in his mouth all night.