(i) Because preceded by not sometimes leads to ambiguity. "I did not write that letter because of what you told me " may mean either "I refrained from writing that letter because of what you told me" or "It was not because of what you told me that I wrote that letter". Avoid this ambiguity by rewriting the sentence.
(ii) To say "the reason is . . . because" is to say "the reason is" twice over, since because is a conjunction that introduces a reason. You may say "I went because I was asked to go" or "the reason why I went was that I was asked to go", but not "the reason why I went was because I was asked to go".
See also Not.