I meant to say that fatigue and headache go along with either syphilis or a viral infection. If syphilis, these symptoms should be gone within a week, even within 2-3 days.
Welcome to the forum.
All symptoms of secondary syphilis should clear up quite rapidly, probably within 7-10 days, and your rash will probably be gone within that time; it may be improving already. However, some of your symptoms are atypical for secondary syphilis. Sore throat is uncommon, and syphilitic mucous patches are painless. These symptoms are more suggestive of a viral infection, not syphilis, and would not be expected to respond to penicillin.
Probably you were tested for HIV, and presumably with negative result or you would have said something about it. However, without meaning to be alarming, your symptoms are consistent with primary HIV -- and since syphilis is one of the strongest predictors of new HIV infection, this has to be a consideration if you are at risk, like unprotected sex in the past 2-3 weeks or so. DNA/RNA testing for primary HIV infection might be in order. Other viral infections probably are more likely, but better safe to sorry, and something to discuss with your doctor.
Good luck and best wishes.