His hens have probably been exposed to whatever he has, so if he is upset about being separated, I would place him a dog crate with food and water back with the hens, but for ease in medicating/handling him often. Sick chickens often do not drink enough fluids, so sometimes wetting the feed can...
Does he smell bad around his beak as well or just around his ears (might be hard to tell?) Is he new to you or have you added new birds recently? He really sounds pretty sick, especailly if both eyelids and ears are swollen, with the head shaking and gurgling. Mycoplasma (MG,) coryza, or even...