Executive summary here is don't install .NET Framework 4.0, or at least not before you install your OCS 2007 R2 bits. If you build up a fully patched new Server 2008 R2 server the .NET 4.0 updates will be included and when you run an OCS install you'll get:
Microsoft Office Communications Server 2007 R2, Microsoft Unified Communications Managed API 2.0 Core Redist 64-bit installation requires Microsoft .NET Framework version 3.5. Installation can not continue.
The solution here is to go in to Programs and Features, and then remove the Microsoft .NET Framework Extended and Microsoft .NET Client Profile packages. Restart the system and you should be good to continue with your installation.