I had gonorrhoea three months back and got the treatment. after that std symptoms like pain in penis, groin,testicle, urge to pee are come and go. 7 essential sti pcr tests are negative. clear watery discharge in morning. what could be the reason?

Of these symptoms, only the discharge indicates anything important. You may have nongonococcal urethritis (NGU), probably acquired at the same time as the gonorrhea. See a doctor (preferably an STI or infectious diseases specialist). If NGU is confirmed, with documentation of increased WBC in your urethra, you'll need additional treatment, and perhaps testing for Mycoplasma genitalium. Good luck.