You've obviously done some research, and I agree with what you've said so far. Also I'd add Ureaplasma to the list of possible causes. I don't think it's that the US in unaware of these infections, just that for some bizarre reason they never test for them, even when there are mountains of evidence which indicate them as causes of urethritis. Then they stick their head in the sand and give out trashcan diagnosis of "prostatitis" or a recurrent UTI.
The doctor who gave you cipro for gonorrhea was mistaken, this drug is not longer a good treatment for gonorrhea due to drug resistance. However, with your negative test, I would not worry about it.
My recommendation is it wait a couple of weeks since taking your antibiotics, do not have sex with anyone, and then test for Ureaplasma, Mycoplasma and Trichomonas. And here's some copy/paste info for you:
Tests are available through LabCorp, they are often not covered by insurance.
Mycoplasma/Ureaplasma, Real-Time PCR
http://www.labcorp.com/datasets/labcorp/html/chapter/mono/vm003300.htm
Number
138778
CPT
87801
Trichomonas vaginalis, Nucleic Acid Amplification (NAA):
http://www.labcorp.com/datasets/labcorp/html/chapter/mono/sm000300.htm
Number
188052
CPT
87798
These organisms are frequently transfered at the same time as the better known STDs like gonorrhea and chlamydia. Gonorrhea has a high cure rate of about 98% (except for resistant strains, where cipro might fail but cefiximine will nearly always work) and chlamydia 96-98%. However mycoplasma/ureaplasma recur about 20-60% of the time. So recurrent urethritis is nearly never due to gonorrhea or chlamydia, unless the patient was reinfected.
Mycoplasma are harder to eradicate for a few reasons. Many strains are resistant to antibiotics, especially tetracycline resistance. This means doxycycline, a commonly prescribed drug, will often fail in treatment. Resistance rates of 50% have been reported for ureaplasma and doxycycline. M hominis is resistant to erythromycin, azithromycin, and clarithromycin. Levofloxacin, another common drug, also has been shown to have a high failure rate for M genitalium. This is why knowing which infection you have is very valuable in determining the correct treatment.
Also, being in Africa, I'd make sure you had a full battery of tests 3 months from now to look for all other STDs, especially HIV.