I don't think you have any kind of STD, based on your symptoms. I don't know much about epidydimal cysts, but cysts are common all over the place and don't mean anything. The small spots you're noticing on your penis are almost certainly cysts, which are normal and unimportant. No doubt you're noticing them because circumstances are calling attention to the penis. I wouldn't worry. Show the cysts to your doctor, share your concerns, and then forget the whole thing.
Best.
Dr. Rockoff