Have you tried running the install from inside a working windows? AFAIK, that is the supported way of doing an "upgrade", but to me, it's not really 100% "clean", since if you keep all the data and applications, etc. than it's not really "clean".
Best bet is to extract software keys using tools like nirsoft's and to extract or sync web based passwords up to google (if they use Chrome), or hopefully get them to use a legit password manager (I use LastPass) to store them. Either way, it makes the password side "recovery" easy...
Then save off the entire "users" space (just in case), since Win10 like to put things into the AppData area before you do the clean install. After that, restore the files, and help the user recover any passwords they can't remember (or forgot to save), since most web sites allow some sort of recovery (usually tied to the email). So if you get that one (i.e. access to email) before you start, you should be OK.
It's not 100% "automated", but it's what I do when trying to help people "restore" things to a clean state.