Migrating WDS from Server 2003 to Windows Server 2012 R2 is for the most part a matter of taking the images you’ve got on your Server 2003 WDS server and importing them on your Windows Server 2012 R2 WDS server.
If you’ve got your 2012 R2 WDS server also hosting the DHCP server role, you’ll need to ensure that you configure the appropriate DHCP options during setup. You’ll also want to make sure that you’ve noted other settings that you’ve got configured. WDS does support answer files, so if you’re using them, you’ll need to bring them across as well.
WDS on Server 2003 does support RiSetup and RiPrep images. Given that everything north of Windows Server 2008 uses WIM, it’s pretty likely that you won’t need those older image formats in the brave new world of Windows Server 2012 R2. Just make sure you don’t spend ages mucking about trying to import image files that you no longer need. You’re migrating to Windows Server 2012 R2 because the product is soon to be unsupported, so the expectation is that you won’t be deploying Windows Server 2003 or Windows XP from WDS anymore.
With Configuration Manager and VMM, the process is somewhat easier. This is because the images won’t be stored locally on the server, but will be stored in each product’s content library. With Configuration Manager what you’ll want to do is retire your existing Windows Server 2003 distribution points and add new distribution points running Windows Server 2012 R2. You can enable the new Windows Server 2012 R2 distribution points to support PXE. You can learn more about configuring PXE with Configuration Manager distribution points on the following web page: https://technet.microsoft.com/en-us/library/gg712321.aspx
If you are using Virtual Machine Manager, you should remove the existing PXE Server and add a new PXE server. You can learn more about the set of steps that you need to take to add a new PXE Server to VMM on the following web page: https://technet.microsoft.com/en-us/library/gg610651.aspx