Urethritis after sex diagnosed with swab. took doxycycline. swab now negative but symptoms remain for 2 months. negative for all sti. what is it?

It's still an STD: If you truly have urethritis -- meaning you have abnormal discharge (not just discomfort or pain on urination) AND you have increased white blood cells in your urethra -- then probably it's continuing nongonococcal urethritis. NGU is almost always an STD, but the exact cause sometimes is unknown. Possiblities include trichomonas and Mycoplasma genitalium. See STD or infectious diseases specialist.

In-person Dr. visits: In-person evaluations by one's primary care doctor and one's urologist can help figure out what may be causing the inflammation. Non-infectious causes are more rare, but do happen on occasion such as rheumatological or psychiatric conditions. A good, thorough evaluation will help... meaning this cannot be figured out online.