I have came up with a much better solution.
Also, after looking on the Adsense site I believe that the use of Iframes does not fit within their policies.
Their policy also states not to edit their code, however, my new method requires separating the code (so use at your own risk, I can not say that this fully complies with their policies)
The Solution:
1. Paste the first <script> section of the code into the additional header content for the entire shop, it should look something as follows:
<script type="text/javascript"><!--
google_ad_client = "Your Publishing ID Here";
/* Product Right */
google_ad_slot = "4606997194";
google_ad_width = 120;
google_ad_height = 240;
//-->
</script>
2. Paste the second <script> section in the product description using the html tool, I used div tag floated right to suite my purposes.
<div style="float: right;"><script type="text/javascript"
src="http://pagead2.googlesyndication.com/pagead/show_ads.js">
</script></div>
Works like a charm. This is a MUCH better method than using the iframes