Are you sure, Anonymous Access is really required for Autodiscover? Actually I'm getting some strange errors when it is allowed (Outlook cannot find the Exchangeserver), which seam to be resolved when I disallow Anonymous Access. This is with a CAS-Array, not a standalone CAS. Could you maybe have a list with the settings for servers in a CAS-Array, too?
Another thing: Could you please make a WARNING that the Authententication methods are for the specific directory ONLY. So they are not necessarily to be inherited by subdirectories. For examle OWA might be fine with just basic authentication, the subfolder OWAauth however requires anonymous access (at least when OWA-Forms-Based-Authentication is used)
No I have not reset the permission for all subfolders, however if I would have issues which I guess are related to the settings listed above I might try to configure my server EXACTLY that way, which would cause even more trouble, when the settings for subdirectories need to be different.