So, after searching for hours on end some months ago, I found a program that does exactly what I wanted in terms of making a standard instrument to use with this game and more. I now have exact rips of every sound from Minish Cap, and exact midi data too, which means combining these two together, you can replicate the music from Minish Cap exactly. It even ripped all the sounds and instruments into a soundfont file, with loop points and everything, and midi loop points too which show up in FL Studio at least.
So over the next couple of months I'll work on using the midi data to clean up and arrange the soundfont exactly as it should be, which will then be required to be used in the music for this game. You can also use the soundfont to get all of the sounds from Minish Cap ever.