Yeah sappy seems not to get the song table. I guess it is stored in a compressed format. If you drop a midi file on the gb2bidi.exe it will output a *.s file with the same name as the midi file. I think together with the MPlayDef.s file you can assemble the *.s file to a binary track you can insert into your ROM. In your case you might need to figure compression first. Then write a tool to compress the binary before you can insert it.
If you are new to sappy you might consider to practice on other ROMs that work. I guess you might also have a hard time arranging midi files and figuring how to arrange instruments to your track.
This is not a plug and play solution it needs some work to convert and insert tracks.
What seems easier is getting music of a other game and insert it again.