GOD DAMN that took a very long time but I finally figured it out. I hate Vista more than ever now.
I'll try and write a guide in case anyone has the same issues as me but I can't guarantee coherency. This is for
Vista users who have done everything in Covarr's guide but still have two sets of music playing, the midi and the music you selected with FF7music. If you try to go into the game's config settings and lower the music volume, you also lose sound effect volume. Here is how to fix that.
1.) First, some house cleaning. This may not be a mandatory step. Go to your User directory. Right click inside somewhere, go to properties, and select show hidden files and folders. Next, go into your AppData folder (it will look like a ghost folder if you are able to show hidden files and folders). Find your VirtualStore folder somewhere in that director. I had to go through AppData > Local to find mine. Inside your Virtual Store folder, navigate to your Final Fantasy VII program folder as if you were navigating to it from your C:\ drive. Delete your SquareSoft, Inc or Final Fantasy VII folder (however you installed it, just get everything). If you were never able to find your Virtual Store folder or the Final Fantasy VII folder within it, great.
2.) Download Highwind. You can find that here:
http://christian59.ch.funpic.de/html/highwind.htm3.) Extract the contents of the Highwind download to a folder, doesn't really matter where. Desktop, user-created subfolder within FF7 directory, whatever. I would NOT recommend the root directory of FF7.
4.) Right click on Highwind.exe and go to Compatibility. Select Run As Administrator.
5.) Open Highwind.exe. Click on Open Archive and find midi.lgp by going to your FF7 directory then Data > Midi. Open it.
6.) Make sure Create Backup is checked.
7.) Click Remove until everything is, well, removed.
8.) Click Save Changes and close Highwind.
9.) On FF7 music, click Run FF7. Tada!