I think both incidents had the same impact. The Swift Boats gave people a reason to not just vote against Kerry, but to hate him. Likewise with F9/11 and Bush. People who swallowed this crap were already inclined not to vote for the person being attack, but both the SBVFT and F9/11 stirred up such venomous hatred of the candidates that any kind of post-election consensus became a pipe-dream.
Here's some articles for anyone still clinging to the biggest lies of 2004 as fact:
http://factcheck.org/article231.html
http://www.factcheck.org/article294.html