I experienced this condition today (HTTP 404 on large file upload with IIS 7) but I thought I had made all the correct configuration settings. I wanted to upload files up to 300MB so I made the following web.config settings in a sub-folder of the application:
<configuration>
<system.web>
<httpRuntime maxRequestLength="307200" />
</system.web>
<system.webServer>
<security>
<requestFiltering>
<requestLimits maxAllowedContentLength="314572800" />
</requestFiltering>
</security>
</system.webServer>
</configuration>
This configuration worked in test but when I copied the updated files including the web.config to the production server, I received the HTTP 404 error on uploading a 90MB file. Smaller files under the application-wide limit of 30MB were working fine, so I knew it was a request size problem of some sort.
I figured there was a chance IIS had cached some application settings and just hadn’t updated them, so I recycled the Application Pool, after which everything worked as expected.