What kind of testing did they do at the clinic? When did the pain start?
It's really hard to say if this is herpes or not. Having internal herpes sores can cause the pain you're in, but there are all kinds of other things that can, too.
Also, there are false positives on the hsv2 IgG, and having a non-specific result like 1.09< doesn't help much. (Are you sure that's what it says?) If it's less than 1.09, it's probably a false positive.
Have you been under the care of a urologist since you got shot in the testicle? If this doesn't improve, I'd give them a call.