All the Manager templates should be under the assets/templates folder.
For future reference, whenever I modify something that comes with MODx, I duplicates it and add "My" as a prefix. That way none of my changes will get overwritten in an upgrade.
If someone has modified a number of the built-in components of MODx without renaming them (or at least making a list of the changes), you are in a world of hurt. Probably the only thing to to is to do the updgrade and see what breaks.
BTW, it’s always a good idea to back up your whole site and the MODx database before upgrading so you’ll have something to revert to and refer to in the future. In your case, it’s critical.
I think you can get rid of the search form by deleting this line from the Modxhost.tpl file:
<div id="search"><!--search_terms--><span id="search-txt">SEARCH</span><a name="search"></a>[!AjaxSearch? ajaxSearch=`1` &AS_landing=`8` &moreResultsPage=`8` &showMoreResults=`1` &addJscript=`0` &extract=`0` &AS_showResults=`0`!]</div>
I think you’ll find a sidebar div in the same file, but you may want to empty and restyle it rather than deleting it unless you want to redo the site’s CSS.
You can use FireFox with the FireBug add-on to see where the CSS is coming from and play with changing it. Definitely worth learning.
I’m not sure which MODx you’re referring to, but in Tools | Configuration, change the site name and see if that does it.
Hope this helps.