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Questions in the Urology forum are answered by Dr. Stephen Liroff, affiliated with the Henry Ford Hospital. Topics covered include benign prostate disease, penis curvature, cystisis, kidney stones, pediatric urology, prostate, sexual dysfunction, urinary tract infections (UTI), and urological cancers.
Oral herpes (HSV1) is possible, and very common. You didn't mention testing for HSV2 (genital herpes) which is also possible.
If after prolonged antibiotics, no improvement, it's less likely a chronic infection such as prostatitis since 3 weeks of antibiotics is often long enough to get rid of that, but sometimes takes a longer course.
Just the act of ejaculation can cause urethral burning, especially the first time you urinate after you ejaculate, which is very normal.
Wife's pap smear has nothing to do with any of this, only to her exposure to HPV.
Strees, caffiene, alcohol can increase urination and make it more uncomfortable.
Intense manipulation from wife is not likely to injure but in rare cases it can.
Ask a urologist for help if this is persistent