It sounds like you have a pretty healthy litter. You likely aren't seeing signs of elimination because the mother is stimulating them and cleaning up after them, as she should be. Normally fading puppies are cold and listless, not restless and whining. Most common reasons for puppies to cry a lot is because they are either hungry (not getting enough milk) or uncomfortable (too hot or too cold.) If you feel like he's running a fever, I've given puppies infant tylenol drops before with no issues. Literally just a drop though. Personally, I wouldn't administer any antibiotics to any puppies without being sure that there is a problem, and then knowing for sure what that problem is. Nine puppies is a large litter, so if he continues to act poorly, it may just be that the mom isn't getting around to giving him as much attention as the others, and some extra milk/stimulation may be all that he needs.