I have had this condition for years now, even before I was sexually active. I have large (pencil eraser) sized almost blisters on and around my scrotum, but not the penis. They are red and hurt to the touch, at first they are hard for about a day, after that they are very soft, and i believe are filled with blood, but they are not protruding. When they go away after about a week or so, it leaves a soft indent in the skin with no redness.
The term "sexually active" is a poor one for Christians to use. It implies an acceptance of sex taking place outside the boundaries of marriage. "But fornication and all uncleanness or covetousness, let it not even be named among you, as is fitting for saints" (Ephesians 5:3).
I could not find anything that matched your conditions exactly. If I had to hazard a guess, it would be that you had some form of cysts, which are not unusual to have on the scrotum. What doesn't match is that cysts tend to be smaller most of the time and tend to last longer than a few days. I doubt it is anything to worry about, but it won't harm to ask your doctor about them the next time you have a wellness exam.