Itching or irritation in the penis can be an STD symptom, but it also can be nothing more than heightened anxiety that makes someone notice entirely normal body sensations. After repeated tests and examinations by your doc, you can be sure you have no STD. Directly to your questions:
1) Many things cause prolonged menstrual periods; STDs usually do not. (Chlamydia and gonorrhea can cause spotting between periods, and occasionally heavier bleeding--but simple prolongation of menstruation is not usually an STD symptom. If your wife is conccerned (not if YOU are concerned, only if she is), she should see her health care provider about it.
2) No STD causes the urine to change appearance in the way you describe. This doesn't sound abnormal. (I have never heard of someone examining his or her own urine in that fashion, and don't know how normal or abnormal urine would react. I suggest you stop doing it.)
3) The modern urine tests for STD are highly reliable.
4) No. But if you remain in doubt, return again to your provider. Or if not certain about his expertise about STDs, get another opinion, such as from your local health department STD clinic. But my bet is that nothing is physically wrong.
Regards-- HHH, MD
It's not uncommon for menstrual cycles to vary, some. If your wife is not on the pill, then this is especailly true. If she is on the pill, then the variation can still be due to very benign things, such as not having taken her pills at the same time each day, missing one, etc. As women enter their perimenopausal years, their cycles can vary even more widely. I wouldn't think of this as at all related to your encounter, though it's probably something for her to keep an eye on, and to discuss with her gynecologist if the bleeding is very heavy, very lengthy, painful, or otherwise regularly and increasingly problematic.
Probably, when you rub urine between your fingers, you're simply introducing more air into the mix and causing it to froth up. I understand you're a bit freaked out by guilt right now, but you aren't doing yourself any good by paying that much attention to your urine.
You should probably talk to your doc if you continue to feel irritated despite the negative tests. Did you take a course of antibiotics for NGU? I understand that it is not at uncommon for that sort of irritation to continue even after an infection is cleared. But, even if you had no infection at all, seems pretty likely that you are paying entirely too much attention to your penis and what comes out of it, right now. Guilt does that to a person. Fear does, too. So, you've got a double-whammy of anxiety going, right now. (You might try just leaving your poor urethra alone for awhile. The constant vigilance can't be doing you any good, and may well be causing even more irritation.)
I'm guessing any competent physician would have caught any actual STD by now, especially given the repeated testing. Real problem seems to be regret.
I think, sometimes, that it's easier to pay all of this attention to real and imagined medical issues than it is to think about relationships, and what they mean, and why they matter, and what the heck we're going to do about them. In a world filled with shades of gray, a clear answer--do I have an STD or don't I?--can seem reassuringly black and white. Whatever circumstances led to your decision to visit a sex worker aren't likely to disappear in the wake of negative tests, though. It's harder to examine those kinds of issues (nothing as simple as peeing in a cup, unfortunately) but probably time better spent.
Physically speaking, I'm sure you and your wife are fine, this time. Best to you both.