Have you tried to run WordPress with the permalinks on IIS without success? After choosing any of the custom permalinks, yu got 404 page not found? Than your problem is in the web.config file. As it is not writable from the web, you should manually update it by adding the following section under system.webServer node:

<rewrite>
		<rules>
			<rule name="wordpress" patternSyntax="Wildcard">
				<match url="*" />
				<conditions>
					<add input="{REQUEST_FILENAME}" matchType="IsFile" negate="true" />
					<add input="{REQUEST_FILENAME}" matchType="IsDirectory" negate="true" />
				</conditions>
			<action type="Rewrite" url="index.php" />
			</rule>
		</rules>
</rewrite>