Welcome to our Forum.  I appreciate your confidence in out site and I'll be glad to comment.  Even before I address your specific concerns however, the most important advice I can give you is to stay off of the internet.  While the internet is a great place for communication, much of the health related statements there are incorrect- they are either out of date, misinterpretation or just plain wrong. 

The doctor you saw did not do you any favors by prescribing antibiotics without testing.  The tests taken following antibiotics may have been compromised by the effect of antibiotics.  How long was the interval between taking the antibiotic, which antibiotics, and for how long)?

Strong smelling urine smell is not a sign of STIs or anything else.  It suggests you are paying more attention to yoru urine than normal. 

Additional comments:

While the timing of your symptom onset is suggestive of STI, your symptoms are atypical. STIs do not cause abdominal pain in men and for the discomfort to be most prominent following urination is likewise uncharacteristic.  Further, while a urinalysis is an insensitive test, that it was normal also does not suggest and STI diagnosis.  Mycoplasma genitalium is an emerging. recently discovered pathogen which may cause urethral symptoms.  Many doctors are not aware of it but you can arrange for testing using an initial void urine specimen. 

My advice first and foremost is to stay off the internet.  Although your symptoms are nor typical, you may want to test for Mycoplasma genitalium.  I would NOT test for Gardnerella.  If your MG test is negative, my advice is to try to move on without continuing concern. 

I hope that these comments are helpful.  EWH

Thanks for the additional information, given the timing of your testing and antibiotics, you can believe your test results which show that you were not infected.  I agree that your symptoms (including the additional ones you report, do suggest prostate problems.  FYI, prostatitis is virtually never caused by STIs).

I do not feel strongly that you need to test for Mycoplasma genitalium

Correct, smelly urine is not a sign of STI.  In women frequent urination may be a sign of a urinary tract infection or STI, not so much in men.

The fact that your casual partner tested negative adds to the evidence that this is not an STI.

The penile pain radiating to your back adds to concern about prostatitis, not STI. 

Hope this helps.  EWH

I would not worry about M. genitalium at this time and see no reason for testing.  I also think you can move forward towards having a 3rd child without concern.

I hope my responses have been helpful. We provide up to three response to each client's questions. This is my 3rd response. Thus this thread will now be closed without further replies.  Take care.  Please don't worry. EWH