Thank you for posting.
FileMaker Server 9 wasn't tested or certified on Server 2008 or any 64-bit OS and there could be issues running it. It may be best to plan for a potential upgrade. Before you have your new hardware, try installing FileMaker Server 11 on a test machine and hosting your databases. This way, you will be able to easily upgrade your software should you need to. Another possibility is setting up a virtual machine on the new server to run a compatible OS. Since there could be compatibility issues, you may want to consider these alternatives before committing to FileMaker Server 9 on the new machine.