A new patch adds CD-quality music, as well as "circlestrafing and the ability to start any episode on any difficulty."
"The tracklist has been replaced with that of the original PC version, so every level has its proper music now," says the developer.
In case you were wondering, the MSU-1 is a custom enhancement chip which allows SNES games to make use of much more data, allowing for vastly improved music.
It's not a 'real' chip and was never featured in any physical SNES games, but has been widely used to augment existing titles with better music.
You can grab the patch here.