I confirmed that the opengl.cfg plugin line is set to VGstream, and the driver settings (which on my version of 7th Heaven are found under OpenGL Driver Configuration, not Aali Driver Settings) don't change the music regardless of what they're set to - i tried VGMstream, FF7 Music, and None, and got the 1998 MIDI's for every one.
This is really bizarre. I haven't seen any other posts with this issue and the 1998 music files don't even exist anywhere on my computer.
edit: and just to make sure, I deleted the vgmstream folder entirely and STILL got the old MIDI's. It looks like the game isn't recognizing the music > vgmstream filepath at all. I have no idea where it's pulling this music from.
edit2: aha! Turns out I had to add the music_plugin = plugins/vgmstream_music.fgp line to the Custom GL Config menu as well. That's why nothing was working, the plugin wasn't loaded so it was defaulting to the base OST.