Whatever is going on, you can be sure it isn't chlamydia or gonorrhea, and definitely not related in any way to your sexual exposure 7 months earlier. Discharge of fluid with bowel movements is fairly common; most likely just normal prostate gland secretions. (Defecation can massage the prostate and express fluid. It doesn't usually mean an infection.) You might have allergy or a respiratory viral infection, the usual cause of pink-eye.
The chlamydia tests are accurate; and most likely the antibiotics would have covered chlamydia, in the slight chance the test missed it. There might be a slight chance of nongonococcal urethritis (NGU), but that also would respond to most antibiotics that your doctor might have prescirbed.
These things are obviously no more than coincidence. Millions and millions of people have new sexual exposures from time to time, millions have prostate symptoms, and millions more get viral respiratory infections. It stands to reason that all those things often happen within a few months of each other. It doesn't mean one caused the other.
You need to follow up with your own provider, both about your symptoms and the protein in your urine. Follow his or her advice. You can be sure you have no STD, and no other infection from your sexual indiscretion. There is no important risk to your health or your wife's health.
Best wishes-- HHH, MD
Two things I forgot to mention:
1. My son has not complained about any eye problems.
2. The penis discharges seem to occur after bowel movements.