Welcome to the forum and thanks for your question. I'm sorry to hear of your very unfortunate experience.
The main issue on your mind is whether you might have HIV despite the negative blood test at 42 days. The answer is no: there is no realistic chance. The standard HIV tests are highly reliable at 6 weeks, and the results ALWAYS overrule symptoms that seem to suggest a new HIV infection. If you had an antibody test, you might want a final test at 3 months, the official interval advised by most experts for definitive testing. But you can be confident a follow-up test will remain negative. For more information about all this, see the thread linked below:
http://www.medhelp.org/posts/HIV---Prevention/RNA-and-oraquick-swab-test-/show/1891685
The vast majority of sore throats are due to viruses (meaning viruses other than HIV), and therefore never respond to antibiotic therapy. I assume your naturopathic doctor thought he was treating you "just in case" it was bacterial (such as a strep throat) -- but it isn't at all surprising it didn't help, and that fact also does not suggest HIV. And as noted above, your negative HIV test proves HIV isn't the cause. The lymph nodes don't mean anything one way or the other: any throat infection can cause enlarged nodes in the neck.
I wish you well, and encourage you to consider professional counseling to deal with the aftermath of the sexual assault. But you can stop worrying about HIV; you don't have it.
I hope this helps-- HHH, MD