I tested the conversion taking the advice in the announcement thread into account to make good preparations and had this working with 100% success and all my libraries (including older versions of the projects) converted in early December. Although we had had the problems with the certificates, and another temporary lapse, there has been no reason not to be able to test this in a safe VM if one really wanted to, we have had almost a month now, although one of course could have wished for more time (I did not think about retesting this before now with all the problem reports coming in).
Yes, right now at least the last nightly has the conversion broken, and one should not try to convert, but a fix has already been announced and should be available to test already late tonight (I am on GMT-9 time zone in Alaska) according to @stambaughw.
@ArtG, there might be one other thing that is messing things up for you: There was mention that you had accidentally installed the system environmental variables. (By my opinion these should not have been checked as default in the installer as they are intended for the developers to make it easy to test things and will override the settings in the paths menu. I have accidentally forgot to uncheck these several times and had to clean up.)
You might already know this, I mention it anyway: The problem is that it is hard to clean up after this; a reinstall with these unchecked does not work alone: If using Windows, you need to first get into the registry, search for the path to the KiCad shared folder in the program folder (typically "C:\Program Files\KiCad\share" for a 64-bit Windows version) and delete all the system environment variable entries in the registry belonging to KiCad.*[Edit: It safer to use the Control Panel, or right click Computer-Properties to delete environment variables, see details further down the thread for directions] Then restart the computer. I have also then made another KiCad install with environment variables unchecked just to be sure, but I am not sure that is needed.
This is likely not the solution to all problems, but if it is overriding your settings, pointing KiCad to different paths than you specified under Configure Paths, it is certainly one thing that has to fixed.