This sounds nothing at all like an initial infection with herpes. Just not at all. Since you are negative for both HSV 1 and HSV 2, I would have expected, since you are looking very carefully, that you would notice some sort of sore, should one have appeared. A negative HSV 1 and 2 antibody test three weeks after the encounter doesn’t mean too much. However, but three weeks past an infecting episode, 50% of people have developed antibody, so at least you aren’t in that group.
As a matter of practice, we don’t treat people without a positive gonorrhea test with ceftriaxone. Different practitioners practice differently, of course. These medicines can cause many troubling side effects and it sounds to me like you could have been experiencing those.
Also, I think that people forget when they have a sexual encounter with a new person, they are in contact with all sorts of germs that another person might have, not only those traditionally thought of as STDs. This person may well have had some virus that causes sore throat and flu like symptoms that you may have acquired.
If you were our patient I would recommend that you sit tight and do nothing for the next several weeks. If you want to test again at 7-8 weeks, that’s fine. If negative at 7 weeks, there is slightly than a 70% chance that your test results will stay that way.
The thigh bumps that you describe do not sound like herpes to me.
You have two more questions if you have additional concerns.