If it can be described as a sharp, jabbing, almost like a needle stick kind of pain, it's likely a vaginal infection, which can be treated with a cycle of anti-biotic medication. Vaginal infections aren't necessarily related to STDs or sexual activity, for that matter. And, they are common among women who presumably have both sets of labias.
I couldn't say that the lack of a labia menora is "bad or abnormal," but, I would say that it is uncommon. Whether this is related or makes you any more susceptible to the condition that you're experiencing, is an interesting question that would be best directed to a doctor.
Regarding this excruciating pain, I suggest that you go to a gynecologist to make sure that there is nothing wrong in there. Just because you don't have an STD doesn't mean that all is well.
Regarding your lack of labia minora, I found this thread on medhelp:
http://www.medhelp.org/posts/Womens-Health/No-Labia-Minora/show/390516
Seems that many other women have this issue - AND LOVE IT!!! LOL so enjoy!