Here is some reading on M Gen. Maybe it will help you.
This a very good question and had been addressed in many studies. Often times persistent NGU after all those treatments can be caused by M. Gen. just as you suspect. The difficult part, as you've enocounterd, is getting tested for it. Testing is usually done in clinical studies or in a few labs via PCR. You may want to speak to your doctor about this and then he/she can order the test and collect the sampled from you and ship it to the lab for testing.
The differenece between NGU and M. Gen is that NGU is a condition cause by bacterial infection, M Gen is one of those bacteria that can cause NGU. M Gen definitely sounds like a possibility given the meds you have taken and the remaining pain.
There are a couple other antibiotics you can try to clear this up. Erythromycine may help. In addition to that you can try Moxifloxacin as a last resort. This is a very potent druge that can have lasting side effects if you're not concious of them. You can speak to your doctor about these and see what he thinks. Please let us know how things go and if you get tested, please let us know what your results are. Many men are suffering from the same issue.