After building, a WCF service in Windows Server 2003, I thought no big deal, for Windows Server 2008. I deployed the service on my Windows Server 2008 machine and started getting 404.3 errors only with my WCF service. After checking that I had all of the necessary dependencies:
I kept getting 404.3 errors, so I started examining IIS to make sure that the right stuff is registered. After not finding anything wrong, I started looking at the WCF installation. I found that my WCF services where not installed. You can do the installation manually by running "ServiceModelReg.exe", which was found at %Windows%\Microsoft.Net\Framework\v3.0\Windows Communication Foundation\.
To check status run: Command: ServiceModelReg -vi Result: The expected result if "Default Installation" next to the features shown, otherwise the services are not active.
To turn on Services: Command: ServiceModelReg -i Result: Installation of WCF services in IIS 7(6)
I was then able to immediately test my service and see that I could get to the WSDL.
Hopefully this fixes your 404.3 issue.