I wouldn't recommend using the disavow tool for this. The disavow tool is used to clean up spammy links that were not gained naturally.
A better solution is to use 301 redirects and redirect the 404'd pages to the new pages that work on your website. That way users will land where they should if they click the links, and Google will still give you juice from those links.
Here's a place to get started on how t do that: https://support.google.com/webmasters/answer/93633?hl=en