It's hard to say what the spots are. As you know, it could be folliculitis, or MRSA, staph, or a host of other things. It's unfortunate that you didn't get them cultured when they were fresher, because you could have a better chance of getting an answer.
The chance of getting herpes from an all-protected encounter is very low - maybe 1 in 10,000, especially if the whole thing lasted 6 minutes.
It would also be unusual for you to have symptoms in multiple places like this. Herpes typically (though not always) appears at the point of infection. To get sores on your belly like that would be highly unusual since that skin is too thick for the virus to penetrate. It's much easier on the mucus membranes, like your penis, anus, etc.
If it's where your pants buckle, I wonder if you have a new pair of pants or a new belt? Maybe you have an allergy to something in the metal on the belt buckle, snap or zipper on your pants. Perhaps it's an older item, and the coating on the metal item is wearing off, and exposing you to the metal underneath it.
I'd be very surprised if this is herpes. I think a lot of your symptoms could be anxiety.
If you get more bumps, get in to get them cultured as soon as you see them. If it's folliculitis, you may need an oral antibiotic or an antibiotic cream.
If you decide to get another herpes test, wait until 12 weeks. There is a decent chance of a false positive, and the more you take, the higher the chance that will happen. It takes weeks, lots of money and untold stress to unravel that. If you are anxious now, really, really consider it before doing more testing. A culture is a better idea if you get more symptoms, as those don't have false positives.