Rename your C:\Maelstrom directory to C:\MaelstromOld. Make a new directory C:\Maelstrom, then add a new directory C:\Maelstrom\games. Open the Itch client, log in with your credentials used to purchase the engine. At the top of the client screen, paste the URL to the game: https://chezjfrey.itch.io/gentlemen-of-fortune-maelstrom-engine
There should be a button at the bottom to "Install". Select your new C:\Maelstrom directory for installation. Then do the same for City of Ships, but install to C:\Maelstrom\games. When the installations are done, you should see two new directories for C:\Maelstrom\gentlemen-of-fortune-maelstrom-engine and C:\Maelstrom\games\gentlemen-of-fortune-lost-ships-city. The shortcuts you get default to 32 bit and we can change to 64 bit, but lets get the automatic update and the config setup working for you first with just these steps.