I'm taking him to a different vet tomorrow to get a culture and switched back to an injectable antibiotic.
He has been in a hospital tank on paper towels for the past 3 month and I did raise the heat to 95 degrees. Starting today I'm bringing his humidity back up too.
The vet gave me a small syringe without a needle to squirt the antibiotics into his mouth which I thought was weird for the same reasons you stated but I followed the instructions because I trusted the vet.
I'll keep you posted and thank you for all your help.