Hi Friend,
As per my understanding,
1. You can replace current licensing with paid licensing. Even you can have multiple licenses added to VC, you could apply whatever is required. Based on applied license, you will be allowed to use features.
2. Once you migrate/relocate VMs to shared storage, You need to have these VMs on ESXi 5.5, then you need to upgrade VM hardware version to 10 in order to leverage all 5.5 features. This can be done using web client (which is one of components of VC 5.5).
Note: I am not 100% sure on VDR. you can even add 4.1 host to VC 5.5 & have shared storage across old and new ESXi. Then vMotion VMs to new ESXi , remove old ESXi, upgrade VM hw version to 10.
Let me know if you need any clarification