Good to hear :)
Except now this is completely redundant (it won't work anyway):

function MyFoom() {
	return DataObject::get( 'CustomSiteConfig', "`MyFooterItemID` = '{$this->ID}'" );
}

simply call $thatItem->MyFooter() to get the SiteConfig that FooterItem is related to.
Although personally I'd call that relation something a bit less confusing ($has_one = ['Site'=>'SiteConfig']; perhaps)

Oops, I meant to delete that, thanks again :)
FooterItem.php

<?php

class FooterItem extends DataObject {
	
	static $db = array(
		
		'FooterText' => 'Text',
		'FooterLink' => 'Text'
	);
	
	static $has_one = array(
		//'FooterImage' => 'Page_Image',
		'MyFooter' => 'SiteConfig'
	);
	
	
	
	function getCMSFields_forPopup() {
    $fields = new FieldSet();
 
    $fields->push( new TextField('FooterText', 'Text' ) );
    $fields->push( new TextField('FooterLink', 'Link' ) );
 
    return $fields;
		}
		
	
	
}