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Pain at the base of the penis and perenium

I am 25 years old and work out regularly.
For about 6 weeks now i have had a constant dull ache at the base of my penis. It first started after some rough sex with her on top. We had to stop because I wasn't feeling right.  For about a week after that I had very tender testicles and had to be very careful sitting and crossing my legs.
The pain spread to the entire groin area especially the left side along the hip crease. I even had pain on the lower left flank by the upper hip bone there. It was a burning pain.  
The testicle pain, burning pain in my hip, as well as the pain in the left hip crease has gone after week 4 but now I am having pain in my perineum and have a very tight pelvic floor for the past week or so. Because of the pain in my perineum I am having on and off hard flaccid symptoms. Also, any time I am getting an erection, I have an ache at the base of the penis on both sides of the shaft.

I went to see my primary car physician and after blood work, urine test and x-rays came back fine, I was sent to a physical therapist for possible pulled ligament.   That was 2.5 weeks ago

The pain is not terrible as it is dull, it is just constant and very debilitating. I have taken ibuprofen on and off but it does not seem to help the pain.

I have had sex and masturbated only a few times since this started. I have stopped though and am hoping to give those muscles a break for awhile. I have also stopped working out since this initially happened.

Has anybody else experienced this and how long does this take to recover from? Does this sound muscular/ligament or could it be more nerve based?
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