After cloning the repo, git submodule must be called inside vimfiles. I would add this step.
cd C:\Program Files\Vim
rmdir /s vimfiles
git clone git://github.com/vgod/vimrc.git vimfiles
cd vimfiles
git submodule update --init
For powershell users ¯\ (ツ)/¯, option /s doesn't work; it should be rmdir <path> or Remove-Item -recurse <path>