Wayfinder is in itself a minor application; it uses a number of mini-templates to control the output of the menu; the default is to generate a simple nested unordered list with several classnames depending on the parameters given in the snippet call. This allows the generation of any kind of menu that can be imagined. You might find this to be of interest.
http://modxcms.com/forums/index.php/topic,34176.msg207851.html#msg207851
What you have found in the cache file is the "row tpl", the mini-template to control the output for each row of the menu. It looks like it was done by someone who doesn’t know MODx or HTML very well; that should look like
<li [+wf.classes+]><a class="root-item" href="[+wf.link+]">[+wf.title+]</a>[+wf.wrapper+]</li>
The [+wf.classes+] placeholder will be replaced with whatever classes are specified in the snippet parameters; by default a class of "last" is applied to the last row of each level, and "active" is applied to the active menu item and its parents if the menu is nested in multiple levels. The menu as it is won’t allow styling of the active menu item, which is really the whole point of using a dynamically generated menu in the first place.
The [+wf.wrapper+] placeholder will be where nested inner levels of the menu are inserted; without it you won’t get more than the top level of rows.
It looks as if the outer set of <UL> tags are in the template itself, surrounding the [[Wayfinder...]] snippet tags. By default, Wayfinder uses a simple "outer tpl" to set the top-level <ul> tags, so another chunk should have been used for the "outer tpl".
Since these mini-templates are usually stored in the database as "chunks", you’ll need access to the MODx Manager to edit them. However, it can also use external .php files to store the HTML code if you prefer; in that case the only parameter to the Wayfinder call would be the name of the configuration file to be used. You can find some sample config files in the assets/snippets/wayfinder/configs folder.