This is a tough problem. Most dogs can go over night by 2 months or a little longer. Much of what you are doing is what I would suggest. You might reduce the problem by cutting out the after after about 7 PM. That, along with getting him off the antibiotics, may help the urinations. He could simply going ahead with the bowel movement while he is out. Post back in a few days and let us know how he is doing. If he is still having problems, I will suggest some other things.
Thank you for giving him a home. It breaks my heart to know how many nice dogs are killed for lack of a good home.