When Spirit was put on the 6 weeks of Amox, the specialty clinic wanted to wait until he had been off them for a week to do a urine culture. I called my vet and she didn't want to wait that long. She wanted to do one at three weeks and then again right after the 6 weeks.
Frankly, after reading what you went through, that made more sense to me and I felt greatly relieved that I wouldn't be sweating it for a week only to find out that the bacteria wasn't gone.
So I hope there is some simple test they can perform for Adam. If not for anything else than to give you a sense of where you are in this battle. I'm praying really hard that you've won the war.
Also, are you doing anything like probiotics? My vet says the protocol is to wait until he's off the Amox and then start them. I found out from the specialty clinic that Spirit evidently has a history of ear infections, so I was worried that the antibiotics would throw his system out of whack. He has been scratching at his ears little bit since we started the Amox.