I would say wait for Alyza to answer that, most likely yes but when you uninstall and start from scratch you need to make sure you've cleanly uninstalled it and removed the registry keys. I'm guessing maybe if you knew the filenames of all the textures and music mods you downloaded, manually created the proper folders and move them into there it could work. Alternatively you could probably uninstall those mods, setup your directories correctly and then re-install them, this will also take a long time because since both your music and texture folders are incorrect (and pretty much most of these mods affect textures, you will probably have to re-install most of them since it looks like you have them mixed up in your main textures folder and not in the mods folder) but I would say wait for Alyza to answer.
If you want to uninstall without waiting follow these steps for a clean start.
-First download
http://forums.qhimm.com/index.php?topic=14421.0 There is the link, it usually deletes a handful of registries left over after uninstall.
- I would then check your steam folder and if the ff7 folder is still there after uninstall delete it.
-Then run CCcleaner
https://www.piriform.com/CCLEANER. Then you're good to go.
Like i said though when you run the 7th heaven converter, right click run as administrator on the executable. Also to turn off UAC either permanently or temporarily type in UAC into your search box. Select Change user account control settings, move the slider to never notify. Disable your anti-virus for the converter and then afterward the converter has finished re-enable your anti-virus add an exception to the 7thheaven.exe and check to make sure it's not quarantined. I know this might seem like a pain in the ass but it's worth it and once you get it setup you can just activate/de-activate mods since they are injected now, no more uninstalling if you want to use a different mod.