When we say "skin to skin" for STDs, we mean direct oral, genital or anal skin to skin, while unclothed.
The skin on your thighs is too thick for germs to penetrate if it's intact (not cut or broken).
When she sat on your face, if she had a syphilis sore on her vagina, and it came into contact with the inside of your nose - a mucous membrane - it would be possible, in theory, for you to get a sore there, but it's not the most likely mode of transmission.
Vaginal and anal sex are the most likely, then oral, then unclothed rubbing and grinding of any of those parts.
Syphilis ONLY causes a round, painless sore in the first stage. Later, you'd get a rash over a lot of your body.
You sound like you have something else going on - maybe covid? - and should see a doctor. While you're there, ask for a syphilis test. It's so easy to test and put your mind at ease. Even if it's not causing your symptoms, at least you'll know you don't have it and be able to put it behind you.
Feel better.