Welcome back to the forum. Thanks for your question.
There are many features of your question in common with the one you asked a little over a year ago. As Dr. Hook said then, discharge with bowel movements isn't rare -- here's the link to a thread that discusses this in detail, which contains a link to yet another thread:
http://www.medhelp.org/posts/STDs/Defecation--Semen-Sperm/show/1608008
As for the "irritated" feeling, in the absence of visible discharge (spontaneous, not with defecation) it is unlikely to reflect any STD; and in any case, it's a bit soon for symptoms related to an exposure only 2 days earlier. I have to suspect anxiety is contributing. Also, having had condom protected sex, the chance of any STD is obviously low -- and it's zero for most of the STDs that could cause urethral infection. Had you been my patient, I doubt I would have agreed to treat you with antibiotics. But at least I hope testing was done first. Once treatment is started, even if you were infected, you'll probably never know for sure.
To your specific questions:
1) Chlamydia chance etc? None; and symptoms definitely too soon. A week is probably the minimum. Same for nonchlamydial NGU.
2) Condom irritation? Maybe, especially if it contained an spermicide like nonoxynol-9.
3) Protection against new STDs while taking the antibiotics? Yes, for a few days, assuming you were given the right drugs. As for protecting a partner, in the event you in fact were infected, that's a little less certain. Maybe not until ~48 hr after starting treatment. What specifically were you prescribed? That said, it is unlikely you were infected with any STD, so these questions probably are moot.
I hope these comments have been useful. Best wishes-- HHH, MD