He is drinking and has been pooping but it's softer than it used to be. I've seen him drink in the last couple days, I gave him a soak and he drank lots of water. I'm very concerned, I'm not sure what to look for to tell what he's got@AshleeSparling, an animal with a bladder stone(s) can exhibit labored breathing and nasal discharge. He would have to be pretty stopped up before you saw these issues on the front end. Is he eating and pooping normally? I would say that this is an unlikely source of the problem but you have said you have never seen him drink water so I would not completely rule out a stone. It would be easy to diagnose via xray next time you have him at the vet.
If you want answers, and are willing to spend the money, talk to your vet about submitting samples for the Chelonian Respiratory Disease Panel at UF. It may give you peace of mind knowing what the problem is but none of these diseases are curable. Knowing what you are dealing with can help you treat the animal and manage the disease for a very long time.
You seem extremely concerned about this guy, I don't want to alarm you with additional possibilities. I have been in your shoes before and even lost animals while waiting for a diagnosis. Ultimately it was discussions with other tortoise keepers that led us to the proper diagnosis and the right vets to deal with the problem. Listen to the husbandry advice you are getting from the group here (temperature and soaks), share your updates here and keep working with your vet.