It sounds like you have no CD audio. I can't remember exactly, but usually the town music in an Y's game is chip tune, and the outside areas and dungeons are CD. Bonk 1 and 2 play fine off the pack-in GoT disc because they have no CD audio, either to HuCards. GoT has no music because its all CD music, but the FX are stored in memory.
I wonder, maybe, about the condition of the little wires than connect the CDROM to the board. They are pretty easy to tear. More than likely though its an issue with the capacitors you replaced. Its probably a problem related to the CD audio as an analog signal, after it leaves the DAC.