Your symptoms could be due to a few different problems. First, I think that a sexually transmitted infection is still very high on the list of possibilities. Infections with bacteria such as gonorrhea or chlamydia can still sometimes produce problems like this that don't show up till months after the initial infection. While this delay in symptoms is not typical of these infections, it is still very possible. Thus the first thing that you should have done is a test for these infections.
It is also possible that this pain you are having when you urinate is a urinary tract infection
. This type of infection is unusual in men and might prompt a more detailed investigation if this is what you have. Pain with urination can also be due to trauma to the penis. It does not sound like you have injured your penis recently and thus, this is an unlikely cause of this problem.
I think your next best move should be to schedule an appointment with your primary care physician
. He or she will listen to your symptoms and perform a thorough physical exam. A simple urine test will look for bacteria that cause these symptoms. If either of these tests are positive, you can be given the appropriate antibiotic to help clear the infection.