Congrats, hope you enjoyed your time with the game^^
The Mystery Key is for a ultra hidden area. Finding that secret is pretty much impossible. Or else it wouldn't be called a Mystery Key after all. In that area is nothing that count towards the 100%, it's just a bonus, so not much to worry about.
As for the bag of coins, I would recommend walking around in town, there might be a new cutscence somewhere.
The farming system is pretty simple to provide a bit of bonus items over time. Once a seed is planted it, you need to be in Alraune form to make the soil healthy for it to grow. Afterwards it grows over time and can be harvested every once in a while.
