Urethritis that became prostatitis to urethritis again

[Anonquestion]

So It started almost 8 months ago as urethritis (urge to urinate often, itchy feeling in uretha/periodic tingling on tip of penis) I went to my Urologist and they took blood work/urine sample but never tested me STD. I have been married for 3 years and have been faithful this entire time. I had crazy days in college where I was young and dumb and slept with many women unprotected. I was never tested after those days either. I do remember after having sex one time it burned to pee but it quickly went away. So what started as the urethritis, progressed to prostatitis (feeling of golf ball between legs) confirmed by Urologist by DRE and Cytoscope as well as MRI. That has since passed and we're back to square one which just urethritis.

Treatment tried:
NSAIDS
Doxycycline
Bactrum
Cipro
(Recently Flagyl/Azithromyacin) which I took a week ago and I seem to be feeing a little better but symptoms still present.  
Any ideas for future treatment? Would the Flagyl/azithromyacin take longer to act? They were 3 Day treatments? Or what it could be? It flared at a big stress point in my life.

My significant other is asymptomatic, we just found out she was pregnant when the symptoms started for me.