I should clarify my statement that "you don't describe any symptoms that make NGU likely". Burning on urination can be due to NGU, but not usually as the only symptom. If there was no abnormal discharge from the penis, NGU is unlikely. In any case, almost all cases respond to doxycycline, so that's good evidence against NGU.
Your symptoms don't sound like those of any STD and you have been tested for all the common things. There are no uncommon STDs likely to cause this, so you can be reasonably sure that no STD is reponsible for the symptoms, and I doubt they have anything at all to do with your recent sexual exposure. I imagine your doctor's treatment for NGU was just as a precaution, since you don't describe any symptoms that make NGU likely. Anyway, if NGU had been the problem, the doxycycline would have worked.
One possibility for pubic area itching is pubic lice (crabs). Itching is the main symptom, and they can be hard to see. Examine yourself closely, ideally with a magnifying glass, looking for the lice themselves (which at first look like flat brownish spots about a millimiter (1/16 inch) in size); or for nits (eggs), which appear as gray or whitish spots attached near the base of pubic hairs.
Aside from crabs -- which can be sexually transmitted -- I see no reason to be concerned about any STD. The comment below suggests it might just be increased irritation of a chronic skin problem. If the problem persists and your own doctor doesn't come up with a clear answer, consider seeing a dermatologist.
Whatever you have, it certainly isn't dangerous. There is no serious health risk here.
I hope this helps. Best wishes-- HHH, MD
By the way (it's still me, the original question asker), I've had an ongoing problem for quite some time now where on the shaft of my penis, I have flaking/peeling of the skin. I think this is a direct result of too much masturbation without lubricant (especially the way I sometimes masturbate -- by rubbing the head of my penis vigorously -- it's a bad habit, I know). Sometimes it flakes off to the point where, if I rub the skin of my penis shaft against a black t-shirt or something just to see what comes off, I can easily see the flaked off skin. If I stop masturbating for a while, it tends to get better and go away. But naturally, as a guy, it's not easy to do that. This only affects the shaft of my penis, more towards the head (and sometimes on the head itself, but not so much), and I have not had this problem in the same area that I'm having the pubic itching. But I just thought you should know in case it's somehow relevant. Thanks again, and thank god for anonymous internet posting because this is embarrassing!