I am upgrading my motherboard of my server to a Threadripper system and want to start with a fresh copy of unRAID because I have been just updating it from version 4.7.  What files do I need to copy over from the current setup to keep my array and my windows VM , I have no dockers.  It would be nice to know there are no remnants of old plugins and files that are not used anymore after the many updates that I have done over the years.

Install the fix common problems plugin and run a scan.  It will pretty much let you know what stuff is no longer required that still exists on the flash drive that may or may not interfere with your system.  Beyond that, any folder in /config/plugins that does not correspond with a plugin you've installed can be deleted.