After much hair pulling, I've gotten these three things to play nice. It's not perfect, but it's a working solution for the time being with the current version of higan. I've only gotten this working with higan v106 but if this is how you want to play MSU1 games, I've mostly got it figured out.
First, make sure the ROM you want to play is patched for MSU1 support and you have all the .pcm files. Mainly these are available from zeldix.net if you're having trouble tracking these down. Nex