Saatlerimi harcadım sonunda WordPress forumlarında bulduğum konfigürasyon dosyası ile IIS üzerinde WordPress multi-site kurulduğunda oluşan 404 hataları tamamen çözüme kavuşuyor. Yapmanız gereken web.config dosyasına aşağıdaki kodu kopyalayıp yapıştırmak:

<?xml version="1.0" encoding="UTF-8"?>
<configuration>
    <system.webServer>
        <rewrite>
            <rules>
                <rule name="WordPress Rule 1" stopProcessing="true">
                    <match url="^index\.php$" ignoreCase="false" />
                    <action type="None" />
                </rule>
                <rule name="WordPress Rule 2" stopProcessing="true">
                    <match url="^([_0-9a-zA-Z-]+/)?files/(.+)" ignoreCase="false" />
                    <action type="Rewrite" url="wp-includes/ms-files.php?file={R:2}" appendQueryString="false" />
                </rule>
                <rule name="WordPress Rule 3" stopProcessing="true">
                    <match url="^([_0-9a-zA-Z-]+/)?wp-admin$" ignoreCase="false" />
                    <action type="Redirect" url="{R:1}wp-admin/" redirectType="Permanent" />
                </rule>
                <rule name="WordPress Rule 4" stopProcessing="true">
                    <match url="^" ignoreCase="false" />
                    <conditions logicalGrouping="MatchAny">
                        <add input="{REQUEST_FILENAME}" matchType="IsFile" ignoreCase="false" />
                        <add input="{REQUEST_FILENAME}" matchType="IsDirectory" ignoreCase="false" />
                    </conditions>
                    <action type="None" />
                </rule>
                <rule name="WordPress Rule 5" stopProcessing="true">
                    <match url="(^[_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*)" ignoreCase="false" />
                    <action type="Rewrite" url="{R:2}" />
                </rule>
                <rule name="WordPress Rule 6" stopProcessing="true">
                    <match url="^([_0-9a-zA-Z-]+/)?(.*\.php)$" ignoreCase="false" />
                    <action type="Rewrite" url="{R:2}" />
                </rule>
                <rule name="WordPress Rule 7" stopProcessing="true">
                    <match url="." ignoreCase="false" />
                    <action type="Rewrite" url="index.php" />
                </rule>
            </rules>
        </rewrite>
    </system.webServer>
</configuration>