It would be very rare to have lesions in the urethra and none on the outside as well. If you did have lesions in the urethra it would be VERY painful. I've heard it described as the worst pain this person has ever had. I do not suspect hsv to be the cause of your discomfort.
A swab test to check for herpes came back negative. I haven't seen a urologist. I should see my family physician.
Have you been to see a urologist?