Seems interesting, never played the game, had to search redstone.
I would start by making the mod. Even better, just to learn go and try someone else's mod and see how it works.
Then, strip its guts out and start from there if a mod from scratch is too complex.
I know some of my plan may not work at all
If a mod can access the file system ( on Windows ), it could access the Arduino directly as the COM ports are opened using the file API.
And as long as the mod can read the in game values you want, you should only be held back by your own ability.
The Arduino task is probably not worth jumping into yet, I would get the mod generating a file or debug info of what you are expecting to see first.