The dark spot sounds like a mole. I wouldn't worry unless you notice it changing color or shape. Then it can be cancerous. The white spots on the back of your penis are most likely the small cysts that are common and normal on the penis. Is is it irritating you at all? Is it bothersome? From your description it really doesn't sound like it.
Hi! I'm a female so I obviously dont have a penis however my X boyfriend had those white "bumps" as well. i use to worry myself sick wondering if they were normal or not. Turns out, they are perfectly normal. In his case they were on the same line as a white head or ingrown hair. Very much normal. As for the dark spot, I'm not sure but i wouldn't worry. U mentioned it has been there for years. If it has never grown or changed in color, I wouldn't worry about that either. I do recommend U go see your family doctor if its bothering you that much. Best wishes!!