Wouldn't be that difficult, use the html include for the header, include a php file, in that php file simply do what your script does, but in PHP/HTML:
Code
<?php
	$hr = date("H");
	$min = date("i");

	if($hr == 00) {
		$color = "#00FF00";
		$message = "It's Midnight!";
	} elseif($hr == 02) {
		$color = "#FF0000";
		$message = "It's two AM!";
	} else {
		$color = "#FFFFFF";
		$message = "";
	}

	echo("<div style=\"background-color: ". $color .";\">". $message ."</div>\n");
?>

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