For the last few months my penis hurts after urinating or ejaculating, not all the time but enough to effect my sex life. I went the sexual health clinic and they found I had NON-SPECIFIC URETHRITIS (NSU). This was treated with some Doxycycline for a week. My partner was treated to. However, I'm still feeling uncomfortable after urinating/ejaculating. I started to drink more water, but that didn't work. I went back to the sexual health clinic for a check up. They did not found any infection.
What's wrong with me... Please help!

A sexual health clinic is not exactly the best place to look for a diagnosis to a urinary tract issue. Except, may be it's free? Get in to see a urologist. No one is going to be able to diagnose you over the Internet. Clearly you don't feel right, so you need to see someone that specializes in male plumbing.