%XXX% is a placeholder for %program files (86)% or something along those lines.
I believe I did see an error message saying that something or other couldn't be found at the C: drive, and I think it pointed down the program file guff path to where VS would have been placed if it had been on the C: drive.
I'm using the the command line (git xxx <guess at parameters here>). "git help" provides a dozen commands, most of which I've never used, and most of the ones I need aren't listed. The "documentation" is horrible, resulting in a web page that only provides overall syntax, but not any parameters, nor any description of the commands. Web searches are needed to find commands, and sub repo juggling was found in a comment somewhere half way through a discussion of failed attempts.
As it currently stands, I can stumble by with git and a frequent "remove everything and download from scratch" approach. For instance, I won't create a new pull request in a (sub) repo before the previous one is done as I don't want to try to juggle several instances of it (and the complete DFHack surrounding it that's required for the sub repo stuff to be tested), as pull requests are frequently requested to be changed, so the local copy needs to be prepared for making changes to be pushed up.