I don't think the medication would affect the eggs unless he fertilizes them. I'd just keep him seperate. Every medication should have a withdrawl period listed on the label.
I wish I could help with a diagnosis, but I've only had chickens for about 5 weeks now. Is he on medicated feed? Did you look up the symptoms of some of the common illnesses? Coccidosis, Maerks (sp?), etc? I would say the lethargy could be a secondary symptom of the stool. Just because you didn't see any loose stool before you noticed he was lethargic, doesn't mean there wasn't any. Does that make sense? I would think loose stool could cause dehydration which could cause lethargy.
I wish I could help with a diagnosis, but I've only had chickens for about 5 weeks now. Is he on medicated feed? Did you look up the symptoms of some of the common illnesses? Coccidosis, Maerks (sp?), etc? I would say the lethargy could be a secondary symptom of the stool. Just because you didn't see any loose stool before you noticed he was lethargic, doesn't mean there wasn't any. Does that make sense? I would think loose stool could cause dehydration which could cause lethargy.