Thanks for the explanations and input folks - it seems all my issues are around the install / update of the DB then. With that, I am going to stick on the clean install and work on that one.
I had SQL CE edition on this new machine (from a VS install) and thus removed all of that, but still got complaints that the MariaDB / mySQL path was not set. I then uninstalled MariaDB, copied the installation binary back into the folder, and am running again. Now it started the Maria DB install but the eqemy_server.pl script runs and says 'no database connection found - running without' - but hey! At least it is running and installing the maps, binaries, etc now! Will update this post as things progress.
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