Upgrading from 1.3.7 to newest - stuck on moving files to new folder and testing

Please help!

Our 1.3.7 site has been hacked, and after cleaning up the mess, we're trying to upgrade. This is shared hosting on a Windows server.

I've duplicated the database to have a duplicate database to work with.
I've created a new subfolder in my inetpub directory and uploaded a copy of the zencart files into it.
I've edited both configure.php files to add the new directory.

All I get when I try to load the site from the new directory is:

Warning: include(store139/includes/auto_loaders/config.core.php) [function.include]: failed to open stream: No such file or directory in D:\Inetpub\store\store139\includes\application_top.php on line 90

Warning: include(store139/includes/auto_loaders/config.core.php) [function.include]: failed to open stream: No such file or directory in D:\Inetpub\store\store139\includes\application_top.php on line 90

Warning: include() [function.include]: Failed opening 'store139/includes/auto_loaders/config.core.php' for inclusion (include_path='.;c:\PHP5') in D:\Inetpub\store\store139\includes\application_top.php on line 90

Warning: dir(store139/includes/auto_loaders) [function.dir]: failed to open dir: No such file or directory in D:\Inetpub\store\store139\includes\application_top.php on line 91

Warning: require(store139/includes/counter.php) [function.require]: failed to open stream: No such file or directory in D:\Inetpub\store\store139\includes\application_top.php on line 124

Warning: require(store139/includes/counter.php) [function.require]: failed to open stream: No such file or directory in D:\Inetpub\store\store139\includes\application_top.php on line 124

Fatal error: require() [function.require]: Failed opening required 'store139/includes/counter.php' (include_path='.;c:\PHP5') in D:\Inetpub\store\store139\includes\application_top.php on line 124

I've checked permissions at the folder level and pushed those down so subfolders will inherit. Everyone has read/execute; owner has read, write and execute.

Here's my includes file:

// Define the webserver and path parameters
  // HTTP_SERVER is your Main webserver: eg, http://www.yourdomain.com
  // HTTPS_SERVER is your Secure webserver: eg, https://www.yourdomain.com
  define('HTTP_SERVER', 'URL');
  define('HTTPS_SERVER', 'HTTPS_URL');

  // Use secure webserver for checkout procedure?
  define('ENABLE_SSL', 'true');

// NOTE: be sure to leave the trailing '/' at the end of these lines if you make changes!
// * DIR_WS_* = Webserver directories (virtual/URL)
  // these paths are relative to top of your webspace ... (ie: under the public_html or httpdocs folder)
  define('DIR_WS_CATALOG', 'store139/');
  define('DIR_WS_HTTPS_CATALOG', 'store139/');

  define('DIR_WS_IMAGES', DIR_WS_CATALOG . 'images/');
  define('DIR_WS_INCLUDES', DIR_WS_CATALOG . 'includes/');
  define('DIR_WS_FUNCTIONS', DIR_WS_INCLUDES . 'functions/');
  define('DIR_WS_CLASSES', DIR_WS_INCLUDES . 'classes/');
  define('DIR_WS_MODULES', DIR_WS_INCLUDES . 'modules/');
  define('DIR_WS_LANGUAGES', DIR_WS_INCLUDES . 'languages/');
  define('DIR_WS_DOWNLOAD_PUBLIC', DIR_WS_CATALOG . 'pub/');
  define('DIR_WS_TEMPLATES', DIR_WS_INCLUDES . 'templates/');

  define('DIR_WS_PHPBB', '/');

// * DIR_FS_* = Filesystem directories (local/physical)
  //the following path is a COMPLETE path to your Zen Cart files. eg: /var/www/vhost/accountname/public_html/store/
  define('DIR_FS_CATALOG', 'D:/inetpub/store/store139/');

  define('DIR_FS_DOWNLOAD', DIR_FS_CATALOG . 'download/');
  define('DIR_FS_DOWNLOAD_PUBLIC', DIR_FS_CATALOG . 'pub/');
  define('DIR_WS_UPLOADS', DIR_WS_IMAGES . 'uploads/');
  define('DIR_FS_UPLOADS', DIR_FS_CATALOG . DIR_WS_UPLOADS);
  define('DIR_FS_EMAIL_TEMPLATES', DIR_FS_CATALOG . 'email/');

// define our database connection
  define('DB_TYPE', 'mysql');
  define('DB_PREFIX', 'zen_');
  define('DB_SERVER', 'DBSERVER');
  define('DB_SERVER_USERNAME', 'USERNAME');
  define('DB_SERVER_PASSWORD', 'PASSWORD');
  define('DB_DATABASE', 'DBNAME');
  define('USE_PCONNECT', 'false'); // use persistent connections?
  define('STORE_SESSIONS', 'db'); // use 'db' for best support, or '' for file-based storage

  // The next 2 "defines" are for SQL cache support.
  // For SQL_CACHE_METHOD, you can select from:  none, database, or file
  // If you choose "file", then you need to set the DIR_FS_SQL_CACHE to a directory where your apache
  // or webserver user has write privileges (chmod 666 or 777). We recommend using the "cache" folder inside the Zen Cart folder
  // ie: /path/to/your/webspace/public_html/zen/cache   -- leave no trailing slash
  define('SQL_CACHE_METHOD', 'none');
  define('DIR_FS_SQL_CACHE', 'D:/inetpub/store/store139/cache');

And the admin/includes file:

 define('HTTP_SERVER', 'URL');
  define('HTTPS_SERVER', 'HTTPS_URL');
  define('HTTP_CATALOG_SERVER', 'URL');
  define('HTTPS_CATALOG_SERVER', 'HTTPS_URL');

  // Use secure webserver for catalog module and/or admin areas?
  define('ENABLE_SSL_CATALOG', 'false');
  define('ENABLE_SSL_ADMIN', 'true');

// NOTE: be sure to leave the trailing '/' at the end of these lines if you make changes!
// * DIR_WS_* = Webserver directories (virtual/URL)
  // these paths are relative to top of your webspace ... (ie: under the public_html or httpdocs folder)
  define('DIR_WS_ADMIN', '/store139/admin/');
  define('DIR_WS_CATALOG', 'store139/');
  define('DIR_WS_HTTPS_ADMIN', '/store139/admin/');
  define('DIR_WS_HTTPS_CATALOG', 'store139/');

  define('DIR_WS_IMAGES', DIR_WS_CATALOG . 'images/');
  define('DIR_WS_ICONS', DIR_WS_IMAGES . 'icons/');
  define('DIR_WS_CATALOG_IMAGES', HTTP_CATALOG_SERVER . DIR_WS_CATALOG . 'images/');
  define('DIR_WS_CATALOG_TEMPLATE', HTTP_CATALOG_SERVER . DIR_WS_CATALOG . 'includes/templates/');
  define('DIR_WS_INCLUDES', DIR_WS_CATALOG . 'includes/');
  define('DIR_WS_BOXES', DIR_WS_INCLUDES . 'boxes/');
  define('DIR_WS_FUNCTIONS', DIR_WS_INCLUDES . 'functions/');
  define('DIR_WS_CLASSES', DIR_WS_INCLUDES . 'classes/');
  define('DIR_WS_MODULES', DIR_WS_INCLUDES . 'modules/');
  define('DIR_WS_LANGUAGES', DIR_WS_INCLUDES . 'languages/');
  define('DIR_WS_CATALOG_LANGUAGES', HTTP_CATALOG_SERVER . DIR_WS_CATALOG . 'includes/languages/');

// * DIR_FS_* = Filesystem directories (local/physical)
  //the following path is a COMPLETE path to your Zen Cart files. eg: /var/www/vhost/accountname/public_html/store/
  define('DIR_FS_ADMIN', 'D:/inetpub/store/store139/admin/');
  define('DIR_FS_CATALOG', 'D:/inetpub/store/store139');

  define('DIR_FS_CATALOG_LANGUAGES', DIR_FS_CATALOG . 'includes/languages/');
  define('DIR_FS_CATALOG_IMAGES', DIR_FS_CATALOG . 'images/');
  define('DIR_FS_CATALOG_MODULES', DIR_FS_CATALOG . 'includes/modules/');
  define('DIR_FS_CATALOG_TEMPLATES', DIR_FS_CATALOG . 'includes/templates/');
  define('DIR_FS_BACKUP', DIR_FS_ADMIN . 'backups/');
  define('DIR_FS_EMAIL_TEMPLATES', DIR_FS_CATALOG . 'email/');
  define('DIR_FS_DOWNLOAD', DIR_FS_CATALOG . 'download/');

// define our database connection
  define('DB_TYPE', 'mysql');
  define('DB_PREFIX', 'zen_');
  define('DB_SERVER', 'DB_SERVER');
  define('DB_SERVER_USERNAME', 'USER');
  define('DB_SERVER_PASSWORD', 'PASSWORD');
  define('DB_DATABASE', 'DB');
  define('USE_PCONNECT', 'false'); // use persistent connections?
  define('STORE_SESSIONS', 'db'); // use 'db' for best support, or '' for file-based storage

  // The next 2 "defines" are for SQL cache support.
  // For SQL_CACHE_METHOD, you can select from:  none, database, or file
  // If you choose "file", then you need to set the DIR_FS_SQL_CACHE to a directory where your apache
  // or webserver user has write privileges (chmod 666 or 777). We recommend using the "cache" folder inside the Zen Cart folder
  // ie: /path/to/your/webspace/public_html/zen/cache   -- leave no trailing slash
  define('SQL_CACHE_METHOD', 'none');
  define('DIR_FS_SQL_CACHE', 'D:/inetpub/store/store139/cache');

So I'm stumped. I have to do this and quickly. Hope someone can help me so I can get this upgraded and a little more secure!

The message is self-explanatory, but I'll break it down:

Warning: include(store139/includes/auto_loaders/config.core.php) [function.include]: failed to open stream: No such file or directory in D:\Inetpub\store\store139\includes\application_top.php on line 90

It's saying that the file at store139/includes/auto_loaders/config.core.php doesn't exist, but it is needed in order to run. The rest of the message is telling you what script is looking for the file.