Seriously, am I crazy? I've played this game on N64 and Dreamcast and I swear they took out/ changed the music to something less interesting in parts, like the opening when they zoom in on the pirate mothership.

If anyone can point me in a direction where I can restore the music, please let me know.

This is the original PC version. Which is why it understandably does not have any tracks which might have been added/changed in the later versions. There is nothing to restore, the game has always been this way. If anything, you'd be modding in a soundtrack from the console versions.

Nintendo version is basically identical with the PC version, just has lower quality graphics and sound. Never played the Dreamcast version, but seeing as it came out almost half a year later, I can imagine they did some changes.