I'd recommend making 301 redirects for the URLs, if at all possible. That way, anyone with bookmarks to your old site will get redirected to appropriate content rather than receiving an error. Google will also see these 301 redirects and begin offering the new links, while keeping whatever existing search engine placement you'd generated with your previous site.
If you really want to go the 404 route, we were able to force any 404 errors across all of our sites to use the mojoPortal 404 page by enabling the commented-out httpErrors section of web.config. It works for us on IIS 7.5 (Windows Server 2008 R2), but might not work in all versions of IIS, so you should test it first if possible before deploying it.