Nick, I am not entirely sure what exactly you are asking for...
A CJ html link generally appears as such :
<a href="http://www.tkqlhce.com/click-2343223-123123" target="_top">acme.com</a><img src="http://www.awltovhc.com/image-123123-123123" width="1" height="1" border="0"/>
You can track links by using server side coding such as PHP to add, in the case of CJ an SID which can be unique as the case as a username, product code/name on your website. So the resulting link will now appear as :
<a href="http://www.anrdoezrs.net/click-2343223-123123?sid=userid_here" target="_top">acme.com</a><img src="http://www.ftjcfx.com/image-123123-123123" width="1" height="1" border="0"/>
You should be alright to strip the URL further, although if you remove the img src, CJ won't be able to support you with impression data, only clickthroughs.
<a href="http://www.anrdoezrs.net/click-2343223-123123?sid=$userid">
I am not familar with all the CJ api's however I assume when you refer to feeds you are downloading something from the Product Search Service API or something similar in which case you will need to run a script to go through each url to search for '?' where you can add in the sid parameter, as a simple example:
<?php
$url = 'http://www.jdoqocy.com/click-12312312-12312321?url=http%3A%2F%2Fwww.borders.com%2Fonline%2Fstore%2FTitleDetail%3Fsku%3D0470029412&cjsku=12312321123';
$track_url = str_replace("?", "?sid=123book", "$url");
echo $track_url;
?>