Probably you had nongonococcal urethritis (NGU). When acquired from oral sex, chlamydia is never the cause; sometimes normal oral bacteria are the cause (i.e., there may have been no actual STD or other abnormal infection in your partner). Doxycycline is one of the drugs of choice, so you were treated properly.
Since your discharge cleared up, most likely the infection is gone. However, your continuing symptoms suggest a possibility of residual infection. Or, more likely, residual inflammation without active infection. Just as a sprained ankle may still ache from time to time long after the sprain seems to be entirely healed, genital discomfort sometimes follows infections, without necessarily meaning that active infection is persisting. In any case, your symptoms are atypical; I have never heard of discomfort only after ejaculation. It could be prostatitis or the male pelvic pain syndrome; the latter is likely due to spasm of pelvic muscles, as a reaction to past infection or as a manifestation of anxiety.
Most likely there is no need to abstain. It is very unlikely you still have anything that could ever harm a sex partner; perhaps you never did. (Those oral bacteria, even if they caused your initial NGU, probably would not be harmful to a partner.) Most likely your symptoms will just fade with time. But if they persist another couple weeks (or of course if discharge reappears), return to your health care provider for further evaluation. In the meantime, I doubt anything dangerous is going on.
Good luck-- HHH, MD
Thank you for your prompt reply. Will continue to monitor for another 2 weeks.
Thanks.