How much is he scratching? And where?
It could be mites, but that's an odd hair-loss pattern for mites. It could be a fungus, or a bacterial infection. The symptoms of bacterial and fungal infections are very similar, and the easiest way to know which is which is to treat for one, and if it doesn't improve, treat for the other.
In your case, since it involves a fairly large area, I'd treat one end of the lesion (the one that it's hardest for him to lick or get his paws to) with a triple antibiotic ointment, available at any pharmacy. Put it on with a q-tip, and rub it in well. You don't want him to get it in his mouth. Treat the other end with Monistat or some other anti-fungal agent, also rubbing it in well with a q-tip. Apply both creams twice a day for several days. One end should improve, and the other may get worse. If one improves, switch to treating the whole area with that cream. Change your clothes and wash your hands well after treating him -- fungus, in particular, is contagious, and a bacterial infection can be as well.
The reason this treatment often works is that applying anti-fungal creams to a bacterial lesion won't affect it much, if at all. Applying anti-bacterial creams to a fungal lesion will allow it to grow and spread, because the beneficial bacteria that help keep the fungus in check are killed off, and the fungus has no competition.
If he's very uncomfortable, you probably need to see the vet again for a possible cortisone prescription, which would ease the discomfort. Just be sure you see an exotic vet -- dog and cat vets are usually a waste of time and money when guinea pigs are involved, and can actually be dangerous.
