Your chances are very low, actually. Even if she has herpes - which I actually doubt - your chances of getting it in a long term relationship, if all you did was avoid sex when she had symptoms, is about 4% a year.
Using condoms can cut that by about 30-50%.
The chances that she got herpes from her ex in 3 protected encounters is very low as well. Her getting it with condoms and then not having symptoms is even less likely.
I don't know what the shooting pain in your calf muscle is, but it's probably not herpes.
You should get tested for other STDs. The chances that either of you have chlamydia, for example, is far higher than HIV, statistically, if you've had unprotected sex recently.