Magento 1.8: Where to Find the Source Code to Edit Title?

The country select box is prepared by the block,

To change its behavior you just need override the function to you local folder like below.

Just copy the core\Mage\Checkout\Block\Onepage\Billing.php to you local folder like

local\Mage\Checkout\Block\Onepage\Billing.php

Now you just need to put the below code in that file see I have added the "form-control" to setClass() function.

its done now your class will be added to the select box.

public function getCountryHtmlSelect($type)
{
    $countryId = $this->getAddress()->getCountryId();
    if (is_null($countryId)) {
        $countryId = Mage::helper('core')->getDefaultCountry();
    }
    $select = $this->getLayout()->createBlock('core/html_select')
        ->setName($type.'[country_id]')
        ->setId($type.':country_id')
        ->setTitle(Mage::helper('checkout')->__('Country'))
        ->setClass('validate-select form-control')
        ->setValue($countryId)
        ->setOptions($this->getCountryOptions());
    if ($type === 'shipping') {
        $select->setExtraParams('onchange="if(window.shipping)shipping.setSameAsBilling(false);"');
    }

    return $select->getHtml();
}

What is contained between <!-- --> is interpreted by the browser as a comment. Even if it may be interpreted by some browsers differently the rule is the same "You cannot have a comment inside a comment".
So your line is interpreted like this:

<!--[if <!--[if (gte IE 9) | (IEMobile)]><!-->]>
  |                                          ||  
  |                                          ||---output
  |--- comment start                         |--- comment end

That's why you see the ]> at the top of the pages. It is interpreted as output.
The correct use of the <if> tags when adding stylesheets is this:

<action method="addItem">
    <type>skin_css</type>
    <name>css/styles-ie.css</name>
    <params/>
    <if>lt IE 8</if>
</action>

So you have to put only the condition inside the <if> tag. the comment tags will be added automatically by Magento in Mage_Page_Block_Html_Head::getCssJsHtml.
So try it like this:

<action method="addItem"><type>skin_css</type><name>css/styles.css</name><params/><if>(gte IE 9) | (IEMobile)</if></action>