Despite your excellent description of the situation, I cannot accurately judge between herpes, trauma of sex, and other possibilities like yeast infection. It sounds like your STD clinic doesn't do cultures for herpes simplex virus (HSV), but relies on the Tzanck test--looking under the microscope for cells that suggest HSV infection. It's a lousy test, and a negative result doesn't mean much; you could easily still have herpes.
For herpes: most common cause of genital ulceration and pain; apparently the provider saw a blistering lesion; improvement on acyclovir. (But the improvement could be due to thhe Monistat if you have a yeast infection.) Against herpes: association with trauma as an obvious potential explanation.
Your plan for blood testing is the way to go. It would be good to have a test quite soon, which you might expect to be negative (for HSV-2) even if herpes is the explanation. You would then need a follow-up test in a few weeks to see if it becomes positive. (If you wait and have only a single test and it's positive, you won't know for sure whether you were infected recently or sometime in the past.)
In addition, you should speak with your partner. Absence of a history of genital herpes won't mean much, because many infected people are asymptomatic and don't know about their infections. But if it turns out he has had it, or any past suspicion of it, that would obviously be a clue about your diagnosis. If there is any doubt, he could have a blood test as well--and he definitely will need that if herpes turns out to be your diagnosis.
Bottom line: If I had to guess, I think herpes is less likely than the trauma and irritation of sex--partly because that has happened before. Penis size probably doesn't have much to do with it; I'm more suspicious about quality and quantity of lubrication. Perhaps monkeyflower, an STD forum regular who is quite knowledgeable in this area, will have a comment for you. Or you might consider posting a question about it in the sexuality/relationships forum.
Good luck-- HHH, MD
grace
Since it sounds like intercourse is often uncomfortable/painful for you, it's especially important to slow down and spend lots of time enjoying each others' entire bodies. See, the tricky part about painful sex is that it tends to be a self-fulfilling prophecy; it hurts, so you tense up, so it hurts more. The next time you already expect it to hurt, so you're extra tense, so it hurts worse... you get the idea. So I definitely think you should avoid intercourse as long as it's painful. Remember that sex is a LOT more than just intercourse. Use toys, hands, mouths, whatever. There are lots and lots of ways to pleasure each other.
And I would also look up vaginismus. That's an involuntary tightening of the muscles around your vagina; basically, it's a physical response to anxiety. It can make intercourse (or any penetration) anywhere from uncomfortable to impossible. Can you have comfortable pelvic exams? Use tampons comfortably? While you can have one and not the others, it's usually more likely that all penetration is difficult. You could check out the book "Private Pain", by Katz and Tabisel, as well as their site, www.womentc.com. Read some of the stories. If this resonates for you, treatment usually is done with a sex therapist and sometimes a physical therapist (to help you tone your pc muscle). Sometimes it's just a matter of education and getting in touch with your body and its sensations; doing your kegels, using fingers or a dildo regularly, masturbating, fantasizing, etc.
If any of this resonates for you and you'd like more specific info (or if I'm completely, totally off base), you could post more and I'd be happy to try to help further. This probably isn't the appropriate forum, though; maybe the women's forum...