First, generally, before any upgrade or migration, we recommend that you create a backup of your databases. With both NPM and NCM installed, you should have two database defined and in use: one db for NPM and another db for NCM.
With that consideration, you should be able to do what you suggest:
- Create a backup of your Orion databases on the External Server 2008 VM.
- Install NPM and NCM fresh on the wiped box.
- During configuration, point NPM and NCM to their respective databases.
To piggy back on what Andrew has said, we also have upgrade instructions in your customer portal that detail the upgrade procedure. See The specified item was not found. for more information.