So I think I found the perfect solution. I discovered that if you put a ? and some unique character after the file name, it forces the browser to get a new version when that version changes.
So instead of:
<link href="css/mycss.css" rel="stylesheet" type="text/css" />
<script type="text/javascript" src="./js/ngen.js"></script>
code:
<link href="css/mycss.css?1.0.28" rel="stylesheet" type="text/css" />
<script type="text/javascript" src="./js/ngen.js?1.0.28"></script>
and since I use php, I create a global with the release in my main config.php and tack that on to the file reference.
$GLOBALS['V_UNIQUE'] = "?1.0.28" // my current release number
<link href="css/mycss.css?1.0.28<?php echo $GLOBALS['V_UNIQUE']?>" rel="stylesheet" type="text/css" />