What is the cause of testicular discomfort?

Hello doctor,

I am experiencing testicle discomfort for the past few days. I got an ultrasound done and it showed: Tiny right epididymal cyst (0.078 inch), and minimal bilateral varicoceles (0.118 inch). The doctor said none of these findings should be causing me this pain or discomfort as it is common for men to have these things. I am on Ciprofloxacin hydrochloride 500 mg for 14 days, I am on day nine of it. When I first took the antibiotic I felt amazing at the beginning, but now the discomfort is on and off but nothing like it was before I took the antibiotic. Hence, I do not think these findings are causing me discomfort. Is it because of the antibiotic that I feel better? And also even when I lay down I have discomfort and varicoceles usually are painless while a person is laying down. I also had a prostate and bladder exam which were fine. Prostatitis ruled out. Also, gonorrhea, chlamydia, HIV, and syphilis results are negative. The symptoms I have right now are: Flank (lower back) pain when I wake up in the morning, groin or inner thigh tenderness, testicle discomfort on the top (epididymis), and not being able to fully empty bladder, frequent urination mostly at night. I am worried about what could be the cause. Kindly suggest to me what can be done. Thank you.