Here is a good article regarding to CRM 4.0 Email Router issues:

http://blogs.msdn.com/crm/archive/2009/01/08/troubleshooting-the-microsoft-dynamics-crm-e-mail-router.aspx

But what I encounterd is not listed.

If you have an error type HTTP 404 (Not Found)

The E-mail Router Configuration Manager was unable to retrieve user and queue information from the Dyamics CRM server. Verify the url ‘http://servername:5555/orgname' is correct. The request failed with HTTP status 404:Not Found.”

Workaround:

Check your CRM deployment properties, make sure these 2 record are not “LocalHost”, better use its netbios servername, ip address or FQDN.

AD App Root Domain, **AD SDK Root Domain**

How to check:

SELECT Id, ColumnName, NvarCharColumn From DeploymentProperties
WHERE ColumnName IN ('ADSdkRootDomain','ADWebApplicationRootDomain')

Post tasks:

  1. Restart IIS.

  2. Restart Microsoft Dynamics CRM Asynchronous Processing Services.