The solution presented in the above site allowed for a single wordpress installation. Here we had two wordpress installations in two sub directories. The solution was to process the request and identify the installation corresponding to which the request was made based on the sub-folder name. Once this was done all we had to do was change directories (for the case where it was needed) and then include the corresponding index.php. We had to chdir because otherwise the working directory would have been the directory where the 404 handler file is located and this could only work for a single installation.
The code used is given below. Copy this and modify for your needs when you have multiple wordpress installations under a domain in IIS and you want Pretty Permalinks for all of them
<?php
$_SERVER['REQUEST_URI'] = substr($_SERVER['QUERY_STRING'], strpos($_SERVER['QUERY_STRING'], ':80')+3);
$_SERVER['PATH_INFO'] = $_SERVER['REQUEST_URI'];
if(stristr($_SERVER['QUERY_STRING'], '/blog/'))
include('index.php');
elseif (stristr($_SERVER['QUERY_STRING'], '/books/'))
{
chdir('../books/');
include('../books/index.php');
}
else
header("location:http://4sometime.com/blog");
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