Welcome to the forum. Thanks for your question.
I'm afraid you are the victim of overly aggressive STD testing that would not have been recommended based on your symptoms and sexual history. Most important, almost certainly you are NOT infected with HSV. The IgM antibody tests for HSV are notoriously unreliable. Given your negative IgG results 3 months after your most recent sexual exposure, you can be certain you were not infected and your IgM result is falsely positive. Below is the link to a thread that discusses HSV IgM testing in more detail. FYI, we never use the IgM test in my clinic -- for exactly these reasons.
http://www.medhelp.org/posts/STDs/Confusiion-over-other-IgM-Herpes-posts/show/248394
I would also judge that the penile irritation symptoms -- once your nongonococcal urethritis had cleared up -- were not at all suggestive of herpes or any other STD. From all the information provided, including the other blood test results, it is clear you acquired no STD during the sexual encounter aside from NGU.
Finally, I have no advice about your liver enzyme anomaly, except that the first step normally would be to repeat the test. But for sure this has nothing to do with any STD or your sexual encounter, so it is outside the topics for this forum. You should discuss it with your personal physician.
Most important is the good news that you can put the HSV IgM test result and herpes out of your mind. You dont have herpes.
Best wishes-- HHH, MD