Most of the time Linked Mode is used for single plane of glass management purpose. (I did not try for migration purpose bcz moving host like remove at source add at destination will take care of agents cleanup)
So would I just stand up the 5.5 server suite independent of the other 5.0 environment, unmanage or unlink my ESXi hosts from the existing 5.0 vCenter instance, and then link them to the new 5.5 vCenter instance?
As you want to recreate Cluster from scratch and not worried about old performance logs then it will be good idea unlink at 5.0 and link them at 5.5
Would probably want to turn off HA and some of the other gadgets before hand so things don't freak out during the process too right? Otherwise do I have the basic idea?
Based on number of hosts you have at source and how many you want to move them to destination by stage wise will give directions to play with HA & DRS settings at cluster level. However disabling HA temporarily is good for migration.
If you can elobarate the scenario by giving number of hosts/Clusters/ResourcePools/VM's/Data stores/Network setup along with criticality level, then we can create logical design with Risks associated.
Based on the actual hardware/product versions - we can create migration strategy and plan.