Alright so I'm finally passed the formatting issues and corruption. Used the SD formatter you mentioned (Which makes it exfat instead of fat32) and then you format with fat32formatter.exe through the command line. No more corruption and app store works!
However now my new issue, when I go to install BOTW (downloaded from wiiuhelper) through wup y mod it keeps saying that it's not a game, dlc, update, etc. I tried many different wup versions and tried renaming the folder, checked the files to make sure the download wasn't corrupt and still it doesn't work. The DLC seems to work though. I read another thread when others had this issue with BOTW and the only conclusion they found is that some SD cards won't install games over 8GB. So I'm gonna try Mario 3D world tonight and see if that works. If I can at least install some games I'll be happy this wasn't a 3 day waste of time.
This is a completely new issue now. Should we close this thread as resolved and make a new one for this issue?