Whenever you don't trust a doctor, get a second opinion. Personally, I don't like when a doctor tells me it's "probably " something without taking some steps to test and find out if it is ... Of course there are not always answers- but if your lymph nodes are still swollen I would definitely go see another doctor.
If you want to calm yourself, get another HIV test- although I don't think the swollen nodes would have any impact and give you a false negative. But if you need to have reassurance, go find out again.
In general, I am sure your doctor was more than competent. Your sore throat etc may be totally independent of your sexual activity-- but go check it out to make sure.