The good news about his allergies is that his ears have cleared up. For a few months, he was scratching his ears and shaking his head a lot. The inside of his ears turned slightly black because of the continued irritation from his rubbing. The vet said a change in color pigmentation isn't uncommon for that and is nothing to worry about.
The vet also found some bacteria in his ears. After trying several different eardrops, both prescribed and OTC, Otomax Otibit Ointment finally cleared that up. Now Popeye's ears aren't bothering him (for the meantime) and they are returning to their normal pink color. Unfortunately, there's the same discoloration on his belly, and since he has to wear belly bands virtually 24/7, it's unlikely we'll have such luck with that area. But the vet assured me that it was just a superficial issue.