Just checking it over it seems that your text 'TagLine Here' is a stylesheet issue - in line 40:
#logoWrapper {
line-height:106px;
}
Change to:
#logoWrapper {
line-height:100%;
}
In regard to the second search function above the categories menu - this is hard coded into your PHP file includes>templates>your_template>common>tpl_main_page.php
<!-- eof breadcrumb -->
<table width="100%" border="0" cellspacing="0" cellpadding="0" id="contentMainWrapper">
<tr>
<td id="navColumnOne" class="columnLeft" style="width: 150px">
<div id="navColumnOneWrapper" style="width: 150px">
<form name="quick_find_header" action="http://qualitytransmissionparts.com/catalog/index.php?main_page=advanced_search_result" method="get"><input type="hidden" name="main_page" value="advanced_search_result" /><input type="hidden" name="search_in_description" value="1" /><input type="text" name="keyword" size="6" maxlength="30" style="width: 100px" value="Enter search keywords here" onfocus="if (this.value == 'Enter search keywords here') this.value = '';" onblur="if (this.value == '') this.value = 'Enter search keywords here';" /> <input type="submit" value="Search" style="width: 45px" /></form><!--// bof: categories //-->
<div class="leftBoxContainer" id="categories" title="Categories" style="width: 150px">
<div class="ctrlsclose"><a href="#"><span class="closeleft"></span></a></div>
<div class="ctrls"><a href="#"><span class="min minmaxleft"></span></a></div>
<h3 class="leftBoxHeading" id="categoriesHeading">Categories</h3>
<div id="categoriesContent" class="sideBoxContent">
<a class="category-top" href="http://qualitytransmissionparts.com/catalog/index.php?main_page=index&cPath=5">Cases</a><br />
<a class="category-top" href="http://qualitytransmissionparts.com/catalog/index.php?main_page=index&cPath=2">Drums</a><br />
<a class="category-top" href="http://qualitytransmissionparts.com/catalog/index.php?main_page=index&cPath=4">Planetary Sets</a><br />
<a class="category-top" href="http://qualitytransmissionparts.com/catalog/index.php?main_page=index&cPath=3">Pumps</a><br />
<a class="category-top" href="http://qualitytransmissionparts.com/catalog/index.php?main_page=index&cPath=1">Valve Bodys</a><br />
<hr id="catBoxDivider" />
<a class="category-links" href="http://qualitytransmissionparts.com/catalog/index.php?main_page=products_all">All Products ...</a>
</div></div>
<!--// eof: categories //-->
The red highlighted stuff is the culprit I believe so hopefully that will help - be sure to back up the file before editing - I am not particularly gifted regarding PHP - but I think this is where your problem lies..
