Quote:
To edit your Theme’s 404 error template file:
1. Open your WordPress admin panel:
2. Choose Design menu. (Presentation pre 2.5)
3. Choose the Theme Editor page.
4. Check to see if your theme includes a ‘404 Template’ in the list of files.
5. Click the link for ‘404 template’ along the right side of the page.
6. Edit the message text to say what you want it to say.
7. Save your changes.
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Or do you want to use your own file all together?
Here's a complete tutorial
http://codex.wordpress.org/Creating_an_Error_404_Page
Edit: I better say this before the 3 minute edit.. You likely want to completely bypass wordpresses 404 handling all together.. I'll be back.