Custom jQuery plugins not working.

Hello all ??

I am trying to convert a HTML 5 theme I found on internet in a fully functional Worpdress theme for a school project.
I am done with the custom post types and the HTML/CSS.

The issue I am having is making the custom jQuery/Javascipt plugins working on the website. These plugins are :

-Background Slider
-Header Slider
-Text Slider
-Image Popout

I am a novice to anything javascript related, so I blindly followed tutorials on how add to my own version of javascript in WordPress. Here is what I added in my Header.

Before <?php wp_head(); ?>

<?php wp_enqueue_script("jquery"); ?>

After <?php wp_head(); ?>

<script type="text/javascript" src="<?php bloginfo('template_directory'); ?>/js/jquery.min.js"></script>
		<script type="text/javascript" src="<?php bloginfo('template_directory'); ?>/js/custom.js"></script>
		<script type="text/javascript" src="<?php bloginfo('template_directory'); ?>/js/slider.js"></script>
		<script src="<?php bloginfo('template_directory'); ?>/js/slides/source/slides.min.jquery.js"></script>
		<script src="<?php bloginfo('template_directory'); ?>/js/quicksand.js"></script>

At first I couldn’t find where the javascrpit plugins where called but it seems to be from custom.js. Each custom javascipt is linked to css markups (stop me if I am talking nonsense i am trying to figure stuff). Here is a part of the code in js/custom.js file :

// Jquery with no conflict
jQuery(document).ready(function($) { 

	//##########################################
	// Nav menu
	//##########################################

	$("ul.sf-menu").superfish({
        animation: {height:'show'},   // slide-down effect without fade-in
        delay:     400 ,              // 1.2 second delay on mouseout
        autoArrows:  false,
        speed:         'normal'
    });

    //##########################################
	// Header nav
	//##########################################

    $(document).mousemove(function(e){
    	if((e.pageY) < 200){
			$("#headernav").fadeIn();
		}else{
			$("#headernav").fadeOut();
		}
   	}); 

//##########################################
	// Front slides
	//##########################################

	$('#front-slides').slides({
		preload: true,
		generateNextPrev: false,
		slideSpeed: 500,
		animationStart: function(current){
			$slideCaption = $(".slides_container div.slide:eq("+ (current-1) +") .caption").text();
			$("#headline h6").text($slideCaption);

			if($slideCaption != ''){
				$("#headline").stop().hide().slideDown(600);
			}else{
				$("#headline").hide();
			}
		}
	});

	// default headline
	$firstCaption = $(".slides_container div.slide:eq(0) .caption").text();
	if($firstCaption != ''){
		$("#headline h6").text($firstCaption);
	}else{
		$("#headline").hide();
	}

	//##########################################
	// Reel slides
	//##########################################

	$('#reel').slides({
		preload: true,
		generateNextPrev: false,
		generatePagination: false,
		next: 'next',
		slideSpeed: 700
	});

	//##########################################
	// Rollovers
	//##########################################

	$('.featured-posts .thumb, .gallery-thumbs a, .work-thumbs a').live("mouseover mouseout", function(event){

		if ( event.type == "mouseover" ) {
			thiImage = $(this).children('img');
			thiImage.stop().animate({opacity:0.3},{queue:false,duration:200});
		}else{
			thiImage.stop().animate({opacity:1},{queue:false,duration:200});
		}

	});

It is surprising because it seems like some of the javascript works but I am not sure about anything.

Do I need to edit anything in the custom.js file or change the way the plugins are called ?

I hope I have been clear enough, and if you need any further information just ask me i will provide anything needed !

Thank you for helping !
Cheers,
Aryahell.