Dr. Klein from the Atlanta RFS office called today, said no issues and gave the go-ahead for the AME to issue. He even called me as well to let me know everything is fine and that he had directed my AME to issue. He directed the AME to put 'issued per RFS' in block 60, which I expect puts it to bed. He cautioned against further alcohol related incidents, and I expect to get a manila folder from the FAA in the future with the same caution statement. While stressful to deal with a situation like this, dealing with the Atlanta RFS office was surprisingly easy and they were quite helpful.
As an aside, AOPA legal confirms excargodog's statement about 61.23. With a current FAA medical, if a new medical application was put on hold or deferred but you have no reason to believe you aren't medically fit to fly (self-ground) then you can continue to fly on the unexpired medical until it expires or is officially suspended/revoked for failure to meet medical certification standards.