I am trying to get a custom web application working under CRM's web directory i.e. C:\Program Files\Microsoft Dynamics CRM\CRMWeb\ on a new server with CRM 2016. The same setup was working fine on a CRM 2013 server, from which we are trying to upgrade.
The path is correct because when I remove any of the DLLs from my custom app, I get correct ASP.net error about the missing DLL. But as soon as all DLLs are correct, I get a 404 error for my custom web application.