@dankcushions My main worry was that the msu-1 file will get entangled with other files, especially if I was to add ,ore msu hacks, but this is more of my paranoia. I also thought it would be more tidy, but if it adds more clicks and I can't use lr-snes9x anyway, I guess I'll pass.
Thanks for your help!

Thanks i'll check it out

Tagged for later reading.

Allright! I got the MSU-1 mods working! They work great!

@darksavior There's more than one Z:LttP MSU-1 mod out there.
Try this one: https://www.romhacking.net/hacks/2234/
It seems to work fine for me, with no overclocking.