3-4 days later, I noticed multiple red bumps, not clustered, on the head of my penis and underside of the foreskin. Bumps did not appear to have any fluid in them. Bumps aren't painful and not itchy, they are fading now. Wondering if being covered by foreskin made them less painful / itchy though. Also had a mild sore throat. After this appeared made an appointment with a PCP, they ran full panel STI tests plus swabbed bumps for herpes. Tests were performed on day 10 after encounter. All tests came back negative. I realize 10 days is before many of the tests become accurate, will be going back in a few weeks. PCP Dr said he thinks it could possibly be syphilis.

To answer your main question the answer is no:  no STI is a likely cause of the symptoms you describe. In uncircumcised men, painless and non-itching "bumps under the foreskin" usually are caused by balanitis -- the name for inflammation of the head of the penis. Most cases are "nonspecific", i.e. no particular cause understood. Retracting the foreskin and washing with soap and water usually clear it up. If associated with blisters and open sores, herpes would be a concern -- but usually would have lesions elsewhere on the penis as well. Sore throat also is generally not an STI symptom. Nor dermatitis around the elbows and elsewhere. Despite your PCP's advice, I doubt syphilis, unless maybe you had another sexual exposure several weeks or months ago:  the rash of syphilis cannot start sooner than ~6 weeks after exposure.

Your own suspicions about aggravating a nonspecific minor skin condition, your allergies, and anxiety magnifying your perceptions all make sense to me.

You don't say exactly what STI tests you had at 10 days. Urine gonorrhea/chlamydia testing was conclusive by then, so those STIs are ruled out. All blood tests take up to 6 weeks for positive results -- although those for HIV always are positive in the presence of HIV symptoms, no matter the timing since exposure -- so you can be sure your symptoms aren't HIV. 

And we haven't even discussed the chance your recent partner has a transmissible STI or, if she does, your risk. All things considered, the chance she has any active infection or that you caught it are statistically low, since you have not yet had symptoms to suggest an STI. However, for peace of mind you'll probably want to have truly conclusive tests for syphilis and HIV after 6 weeks. (Or you could have a conclusive HIV RNA PCR test at any time -- conclusive 11 days after the last possible exposure). Don't get tested for herpes:  the blood tests are not entirely reliable and often given misleading (and anxiety producing) results.

I hope these comments are helpful. Let me know if anything isn't clear.

HHH, MD