Welcome to the forum and thanks for your question.
I agree with your doctor: the combination of a negative RNA test and antibody test, at the times you had them, is 100% conclusive proof you did not catch HIV. As far as I'm concerned, there is no need for any additional testing, at 12 weeks or any other time.
Below are links to two threads that go into detail about window periods with the available tests, including a discussion why official advice remains offical advice from most agencies despite clear evidence for earlier conclusive results.
http://www.medhelp.org/posts/show/1704700
http://www.medhelp.org/posts/show/1891685
I hope this has helped. Best wishes-- HHH, MD