Welcome to the STD forum.
You have had accurate replies on the STD, HPV and herpes community forums. Your symptoms are not typical for any STD. You have been grossly over-tested. My guess is you have waste $1,500 or more on tests that you didn't need. But the results are negative.
You describe only one symptom suggestive of any STD, and that is the single episode of white urethral discharge. However, a single such event is unlikely to be due to NGU. Did that event occur not only after urination, but perhaps after a bowel movement? This is often a normal event in entirely healthy men; see this thread:
http://www.medhelp.org/posts/STDs/Semen-Leakage-Question/show/684727
To your specific questions:
1) All your tests are conclusive.
2) HPV doesn't cause symptoms like you describe.
3) See above about the episode of penile discharge. These other symptoms -- dark or strong smelling urine, skin changes -- cannot be cause by NGU or any other STD.
4) EBV does not cause any of the symptoms you mention.
5) I recommend no further tests at 6 months or any other time.
Apparently you have seen two doctors, and it seems both have found nothing abnormal. Your symptoms don't really sound abnormal either; I think heightened anxiety is making you notice various normal sensations and skin spots. You have no STD or any other infection from the sexual encounter last may. It's time to just forget it and move on.
Regards-- HHH, MD