my advice is to take a look to see if there's any redness or any other skin irritations, broken skin, or skin thats partially shed. That should help to id the problem.
Mites can be a real pain and love moist places you can usually see them walking around, check out some online vids of the biting/ nascent kinds, Springfield are ok to have.
I did note kicking, puffing up and swatting around his head, seemed fairly consistent with shedding, but I'd definitely take a look to see whats going on.
One more thought...you may want to try to widen and deepen your water bowl, it also may help him to really soak off his skin. I've got one toad that likes to stretch out and seemed to enjoy my dogs old water bowl lol