Thank you for the post.
If this is a fresh installation of Windows Server 2008 R2, then remove IIS and delete the inetpub folder located on the C:/ drive of the computer. Afterwards, use the FileMaker Server 13.0v5 installation to enable and configure IIS for our instance of a Web Server.
The following is from page 68 of the FileMaker Server 13 Getting Started Guide:
"The IIS web server must be enabled on the master and worker machines in order for FileMaker Server to operate. The FileMaker Server installer installs the Microsoft Application Request Routing (ARR) extension for IIS, if it is not present. If the ARR installer detects that IIS is not enabled, it will enable IIS."
As long as the computer has an Internet connection, the FileMaker Server 13 installer should be able to configure IIS.
Please let me know if any of the above requires additional clarification and keep me updated with any progress.