Not to worry, in my opinion. As per your description of symptoms and your MDs diagnosis, it would appear that you don't have any thing, serious to worry about.
However, Since you masturbate, & sometimes frequently, I would double-chk on any product you may be using, to masturbate with. Certain lotions or potions used in this activity can cause the symptoms, you've described, due to certain additives that will adversely affect the skin. Also, dry friction can be irritable to skin, as well.
I cant say what it is, but from description and based on your sexual history its not an STD. Put the STD worrying to rest.
I think you have a little irritation and lot of anxiety. What you describe doesn't sound anything like herpes or any sexually-transmitted disease. You already saw a doctor who told you this, so there's not really much I can add. Masturbation or any other kind of friction will aggravate this, of course. You need to avoid rubbing, picking, or closely examining your penis. If you're still worried, see a doctor again.
Best.
Dr. Rockoff