Urine, swab and blood tests clear for sti. was told it was epidymitis and finished 2 weeks doxycycline. pain persist in testes, back, abdoman? help

Not epididymitis (?): Epididymitis doesn't cause pain in both testicles (usually only one testicle, with marked swelling and tenderness). It also doesn't generally cause back or abdominal pain. These symptoms are more typical of chronic pelvic pain syndrome or nonbacterial prostatitis (there's an excellent Wikipedia article). Most prostatitis/CPPS doesn't respond to antibiotics. See GUM specialist, eg NHS GUM clinic.

Re-evaluate. : If two weeks of Doxycycline failed to resolve your symptoms, then you need another evaluation to assess the accuracy of the diagnosis and appropriateness of the choice and duration of antibiotic.