Skunk spray can be concentrated enough to cause ulcers on the skin, but I wouldn't expect to see it happening so long after the fact.
As our veterinarian friends say, the skin really only has one way to react to damage...it gets red, ugly, and often loses hair in the damaged area. There could be a number of reasons for the appearance of this type of symptom, including allergies or external parasites, like fleas or mites.
My advice would be to set up an appointment to see your veterinarian so that he or she can see what is happening and potentially set you up with the right medications or shampoos. You can also think about posting your question about skunk spray causing the redness on the skin in the Ask a Vet Expert forum. There are several veterinarians there who enjoy discussing skin cases and can probably offer you some helpful advice.
I work at a dog groomers and we had a dog come in that had peeling dry irritated skin and hair loss. The owner said he got into the swamp so it might be that. He failed to mention that he bathed him his self after. When we sprayed him down to get wet before we bathed him, he sudsed right up. The shampoo wasnt totally rinsed. Make sure he is good and rinsed and see if that helps. Dont use soap unless its special fro sensitive skin like an all natural thing. All the best.