Crafting changes apply on existing games. There's no need to restart.
Well, I used the GoG install. It created a docs, game and support folder above Data.
I'm not sure what you mean by that. But to install the mod you have to copy the 'Data' folder of the mod (after unpacking the file) into the main directory of your game. The result should be: Divinity Original Sin Enhanced Edition\Data\Public\Shared\Stats\ItemCombos for EE and Divinity Original Sin\Data\Public\Main\Stats\ItemCombos for Classic version (I doubt Baardvark's crafting file would work for Classic version due to different data; the result could be the game crashing or just some recipes not working).
Please don't install this mod different from Baardvark's description.