Lisa, from all the descriptions you gave, it sounds like fleas causing the hair loss. The not looking so good in the face is likely due to his URI. He likely had some running eyes where the matter dried and then dust stuck to it. What was stuck to his nose was probably some clumped, dried mucous that got some fur or dust on it. The matted fur would be due to his not grooming so well, or overgrooming. If fleas were bothering him, probably it was due to overgrooming. If due to not feeling well, it would be because he was just so tired from the illness to do a lot of bathing. Humans are like that too when weak from an illness- mostly staying in bed a few days and not showering due to feeling too weak or sick.
The fact that he got up on the shelf and tore into the bag of food to eat is a great sign that he is getting better from the URI. It also is a sign that he needs more food put out for him.
Fleas are hearty critters. The ones out in the yard subject to
several days in a row of below freezing temps- day and night- will die, but those that stay on a warm body, can survive. Flea eggs in a sheltered place will survive just about anything or else there would not be any fleas at all in places that get very cold.
As Mark said, you can give Scruffy a Capstar pill. That will kill any live fleas on him. Even if you are not positive it is fleas, you can still give a Capstar pill. It is not a prescription treatment. They might have it at your local pet store, but if not, the vet's office probably sells it.
Regarding going out to yard through the gatehouse, you might try making a barricade near the door, then carefully slip out to feed the strays in the morning.
Walking on the floor in the gatehouse to go outside and then back into the house is so very unlikely to bring in a URI to the inside cats. I think it is not possible. URI's are airborne, so the great contagion risk is if the sick cat is mingling with the healthy cats where the sick cat sneezes near the healthy cats, or if the sick and healthy cats share food and water bowl. Certainly, after you handle a sick cat you should wash your hands before touching the other cats, but taking shoes on and off would not be necessary over a cat having a URI.
If the cat has ringworm causing the hair loss, then yes, hairs could be contaminated. Instead of your husband taking off his shoes, maybe put a mat in front of the door into the house and make him carefully wipe his feet.
maybe he left the hair alone when he was outside because it was the only thing keeping him warm. now that he's inside, he can work it out. I'm grasping at straws here.
Maybe.
Hair loss is not a horrible disease. Glad you are taking him to the vet. Good luck!