My guinea pig has crusty skin sores. What's the cause and treatment?

In my experience the huge majority of skin issues in guinea pigs falls into two categories: mites and fungal. It's uncommon to see flaking skin and hair loss without it being one of these disorders.

Ringworm would be a concern and is very common in guinea pigs. Instead of being a worm, it's actually a skin fungus, and doesn't always have the classic "ring" shape. The only way to diagnose ringworm in guinea pigs is doing a fungal culture where you collect hairs and put them on a culture medium. It can take 10-14 days to get a result, though most positives show up within the first week. If you don't want to do the testing then what you can do is treat those scabs with an over the counter anti fungal cream like clotrimazole. It is basically jock itch cream. Apply a thin layer 2 times a day. It won't hurt anything if it is not ringworm but if it is ringworm, it will help.

If you are going to shampoo him I would use a medicated shampoo like this one:

https://www.1800petmeds.com/Malaseb+Shampoo-prod10667.html

Lather it on, let it sit for 5-10 minutes and then rinse. The contact time of the shampoo is very important! This shampoo has an antifungal agent in it as well as an antimicrobial agent.

If you try the ringworm cream and shampoo and it doesn't help at all within 7-10 days then I would recommend you get a second opinion from another vet and find a vet that specializes in treating exotic pets as he may have skin mites.

Skin mites in these pets will always cause itching, sometimes severe enough to lead to seizures. If he is itchy then skin mites are very likely. Skin mites need to be treated with Ivermectin injections spaced 10-14 days apart and need to be done by a vet. Usually 2-3 injections are needed to clear the mites.

If your vet doesn't specialize in treating exotic mammals/pocket pets then I would suggest you find one that does. I found this vet in your area based on your zip code:

http://www.acsevh.com/

I hope this helps. Best wishes!