I agree with Xhost, you can forget about HIV.
Doctors often don't know (or care) about the side effects of the medications they prescribe.
Do your own homework, there are many websites with the info.
My assumption is that you were testing at intervals during the entire 6 month period that you spoke about in your original post. If that is true, and your tests all came back negative, then no, HIV is most definitely not "just now kicking in", as you stated.
The conventional wisdom is, at this point, that a 3 month test after your last unprotected sexual encounter (vaginal or anal sex, without a condom) is more than sufficient to accurately and definitively tell you your HIV status. Meaning, of course, that a negative test at 3 months is pretty much all you need - end of worries, you are negative. No doubts, no what ifs: you are negative.
As you have probably tested out to the 6 month mark (which was three months more of testing than you actually needed), I won't even get into the whole 6 weeks/3 months debate. The simple fact of the matter is that you have tested negative well outside of the window period, and, as such, you may rest assured that you do not have, cannot have HIV. End of story.
Whatever is causing your discomfort, it is not HIV. You may wish to visit your doctor and ask for a workup for peace of mind, but certainly, put HIV out of your mind.