If it's an allergen, I would probably do a rinse down. I don't know about shampoo. Unless it's a very gentle, tearless type and you can avoid getting it in the sores, I would probably just do a rinse. You could also put a small cup of baking soda in with the bath water. Though again, I'd avoid getting it in the sore.
There's not much else I would do with the open one besides rub the gunk off with a warm wet towel and put on some neosporin. It really just needs an antibacterial and access to the open air without him scratching or chewing at it.