So even with the "universal update" I'm not on the latest version of the game and when I try to use my serial in the Klei updater I am told that I have an invalid key. Is there a time limit on the GoG key or something of the sort? What might I go about doing to solve this so I can get the latest version?

Try to run the updater with admin rights or with the user account, you used to install the game (which has admin rights, cause otherwise the GOG installer would've shown an error message).

Previous advice solved the problem. Thank you.