What file and folder permission changes does the Microsoft Web Platform Installer make when it installs Drupal?
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However, a manual install of Drupal has a few variables.

For all versions of Drupal you will need to install PHP.  The recommended way to install PHP is with Fast CGI.  (That is also how the WebPI installs it.)

Since you are running Server 2008, it is recommended that you use Mirosoft's URL rewriter if you want clean URLs.  (That is also how the WebPI installs it.)  If you are using Microsoft's URL rewriter, it will automatically look for a web.config file.  Drupal 7 ships with a default one, which I believe will work for Druapl 6 as well.

Then, you need a database.  For Drupal 6 your only practical option is MySQL.  For Drupal 7 you can choose between MySQL and the more native MSSQL.

Once those three items are installed you are pretty much left with permissions.  By default IIS uses C:\inetpub\wwwroot\ for all web served files.  For IIS to read those files the local IUSR account needs read permissions.  To write the local IUSR account needs write permissions.  I believe the recommended behavior currently is IUSR gets read permissions to everything in C:\Inetpub\wwwroot.  However write permissions are restricted to only where absoultly needed.  The traditional location is ..\sites[sitename]\files as that is the default location for user uploaded files.  However Drupal 7 has a fancy web installer for modules.  For that to work ..\sites[sitename]\modules and ..\sites\all\modules need to be writeable by the local IUSR account.  One final note.  For the default Drupal install process to work ..\sites[sitename]\settings.php needs to be writeable by the local IUSR account.  However, post install it is usually recommended that file be read onle.