On those mysterious black spots, my roosters have had those from time to time. They are different from pecking spots, which almost all chickens get once in a while when the pecking order adjusts itself. These mysterious black spots are more like pimples and they are almost always perfect dots, not the formless shapes pecking causes.
One time I was curious what was inside and I scraped one with my fingernail. It had a very scant amount of liquid in it. We're talking spots as small as most freckles on humans or even smaller. I put Blu-kote on these black spots whenever they would appear, and they would clear up in just a couple days, almost never coming back on the same rooster. And it's always been roosters I've noticed having them, never hens.
I've searched for an official explanation for years, and have never come across one, although it seems very common that people report them here on BYC over the time I've been here, nearly nine years. I've concluded they're harmless, whatever they are.