The Vets I work for learned at Las Vegas that you should bath dog on last day and day after to get rid of any left oocysts. We have been seeing a lot of resistant giardia lately.

He was completely asymptomatic until he was diagnosed and ever since the first treatment, he's had stool issues. He's also become picky with his food and I'm not sure if it's from the giardia or teething.

If a dog's stool shows giardia but has no symptoms there is no reason to treat, many dogs are carriers and only have symptoms when their immune system is young. It may be possible that the stool issues you are seeing are being caused by the antibiotics. His lack of appetite could also be from his medication or the self treatment your giving him.