I always run Haxchi first, and I've tried running Mocha as well, but it doesn't make a difference. But when I inject anything (no matter whether I'm changing the dark filter or widescreen settings or not), even if I'm just trying to inject Super Mario 64 into itself, everything works properly and the files pack up, I'm able to install them with WUP Installer, but as soon as I try to play them it gives me Error Code: 199-9999 on my Wii U. I've got my Wii U all set up so I can play anything from Wii U USB Helper, including the official N64 game files. MERGED the issue I'm having is 'Error Code: 199-9999'.
Keep all your unpacked folders in their own folder, and then you can use those as your bases. I used Wii U USB Helper to download the official files, then you right click on them and say 'Unpack'. I was having the 'Base is Invalid' error, what you have to do is unpack the official VC files.
