Nerve like pain in tip of penis, abdominal area, occasional itching on sides of penis. no discharge, blood or anything of that sort. negative for uti, cytoscopy normal, normal pelvic ultrasound, normal std testing. went away came back. hpv related?

Not HPV: HPV infection never causes pain or discomfort of any kind, except sometimes if warts are large and become infected. Possibly the male chronic pelvic pain syndromes (CPPS), sometimes considered a form of non-infectious prostatitis. Or just genitally focused anxiety? In any case, this doesn't sound like anything that will ever cause harm or complications. See a urologist if you remain concerned.