Pretty easy fix:
1. Rename the game rom file as "cart.rom", this is mandatory for all MSU-MD games in the MegaCD core.
2. The second step is also very important: The MegaCD Mister core expects that that CDDA music starts as "TRACK 01" and not "TRACK 02" (for MSU-MD). So change all the entries in the .cue file, starting with "TRACK 01" and it ends with "TRACK 24". The WAV names can be still named as they are.
But the normal SRAM saves (3 slots) aren't working via MegaCD core. Can you please implement proper save support, so that the MegaCD core can use the 3 save slots properly too?
Another option would be: Make support for MD+ music. The normal Mister MegaDrive core supports it now, and SRAM should work then fine too.