If you want a custom version of TheIsland AND new mechanics, then what you’re gonna wanna do is move all the contents of Maps\TheIslandSubmaps (I think you can just move the whole directory) into the Mods\YourMod folder, and in the WorldSettings of TheIsland.umap, set a subclass of the PrimalGameData (which you should put in Mods\YourMod) into the “Primal Game Data Override” property. Then cook your Mod, with the map TheIsland in the “Maps to cook” textbox. It’ll be a verrrry long cook because TheIsland is quite huge, but it should eventually finish. Anyhow, the Steam Upload should give more output than that either way, so it’s very strange that it would hang for some reason. We’ll see if we can reproduce that.
However, consider what is it about TheIsland that you want to change necessarily, would it really require recooking TheIsland itself? For example, if you just want farmable Cannabis seeds, those could be droppable or harvestable via additions to the PrimalGameData Override, and not actually require modifying/recooking TheIsland itself?