Hey, I don’t think you’re looking for the answer anymore, but just in case anyone else comes across this with the same question, I resolved mine this way:
1. Press edit on the plugin page.
2. For the ‘categorized-tag-cloud/categorized-tag-cloud.php’ file, search for this line:
$out .= '<span id="'.$plugin_name.'-el-'.$i.'">'.$tag.'</span> ';
3. Add in whatever separator you want just in front of ‘</span> ‘. So for example, if I want the separator ‘|’, the line becomes like this:
$out .= '<span id="'.$plugin_name.'-el-'.$i.'">'.$tag.' | </span> ';
4. Save and you’re done.