Did those ever look like blisters at any point? It looks alot like fowl pox, which if it is, will just have to run its course. Dry pox are typically caused by biting insects and wound contamination. If that's what it is, there really isn't much you can do for it, other than wait for it to go away. There is a vaccine for fowl pox, but its usually administered to day old chicks.
I'm not certain that's what you've got going on, I've never had it. But, I Googled "brown spots on rooster's comb" and looked through a bunch of images that are very similar to your picture and they were all of birds recovering from pox...