I figured it all out. I ran the drop_player.sql on the newly installed server and then exported my old database based on the drop_player.sql criteria using HeidiSQL. It gave me one clean .sql file with all my character tables.
The one thing you have to be careful of is exporting your character tables using the "same as source", otherwise if you choose something like ANSI SQL you'll run into import problems/errors during your import.
My reasons for keeping two databases on two different machines is that I can rotate the server whenever I choose to upgrade; I never have to worry about destroying my server as I will ALWAYS not only just have the backup character tables but a backup server as well. Then the updates become stress-free.
Hope this helps anyone wanting to update their server but are afraid of messing it up.
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