Presumably, the condom would protect you against std's. I think it never hurts to do routine STD screening but you had what is called safe sex. There is no reason to suspect your symptoms have anything to do with your encounter other than the anxiety you have from it.
Gastrointestinal and stomach issues are often tied to anxiety, yes. I would assume so but you should make sure that something else isn't going on. If all you did was have oral sex, unprotected, you would not have HIV. HIV is transmitted by unprotected vaginal or anal intercourse or sharing of IV drug needles. You also proved this point by taking a test which is negative. So, whatever is going on with your stomach and abdominal tract is not related to HIV.
"my doctor say these results are conclusive ..." so you need to accept that good news and move on from HIV. Billions of negative people like you get those symptoms, not just people who had sex so there is no reason to connect them up with an HIV theory.