There are numerous valving and stack differences, but the major upgrade was in '05 with the offset front axel lugs on the forks. This changes the front end "bite". It was very noticable for me personally.
This is a link to a pretty good comparison of the changes between 03/04 & 05 models.
http://crfsonly.com/specs-04_450-05_450.php
I'm trying to find out if the showa shocks are the same........