Multiple Loops Additional classes Pagination help

I have been coding themes for the past years but I’m not really an expert in php. I hope someone can help me about this problem:

I have four loops in index.php

1st: featured category posts carousel (which is already working way before)

2nd: Certain cat post, 1 post_per_page, with additional class in most parent div

3rd: Certain cat posts, 2 post_per_page, with additional class in most parent div

4th: The rest of the posts, with additional class in most parent divs, hould do_not_duplicate posts from above category except for featured

then I want the 4th loop to be paginated — like page/2/ will show the next page of the rest of the posts (aka recent posts) in the 4th loop.

Here is my code

<!-- start content -->
<div id="content">
	<?php if(is_home() && !is_paged()): ?>
    <?php // Featured posts go here.
    include (TEMPLATEPATH . "/featured.php"); ?>
    <?php endif;?>
    <?php if(is_home() && !is_paged()): ?>
    <div id="highlightcat1">
    	<h3 class="head">Latest Projects <a title="More Projects Updates" href="https://ygladies.com/category/ygladies/projects">more+</a></h3>
		<?php if( $themesbyrozeh_settings['highlighted_cat1'] ) : ?>
        <?php query_posts('posts_per_page=1&cat=' . $themesbyrozeh_settings['highlighted_cat1'] ); ?>
        <?php while (have_posts()) : the_post(); ?>
        <?php $do_not_duplicate[] = $post->ID; ?>
    	<div class="post ptop red">
            <div class="feat">
                <?php
                // Must be inside a loop.

                if ( has_post_thumbnail() ) {
                    the_post_thumbnail('ptop');
                }
                else {
                // nothing here
                }
                ?>
                <span class="date"><?php the_time('d F y') ?></span>
            </div>
            <div class="entry">
                    <div class="entryinfo">
                        <?php edit_post_link('Edit', '<span class="edit">', '</span> -'); ?> <span class="author"><?php the_author() ?></span> - <span class="sdate"><?php the_time('d/m/y') ?></span> - <span class="comment_count"><?php comments_popup_link('0 Comments', '1 Comment', '% Comments'); ?></span>
                        <h2><a href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></h2>
                    </div>
                    <p><?php echo limit_words(get_the_excerpt(), '30'); ?>.</p>
                    <a class="readmore" href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title(); ?>">Read More &rarr;</a>
            </div>
        </div>
        <?php endwhile; ?>
        <?php endif; ?>
        <?php wp_reset_query(); ?>
    </div>
    <?php endif;?>

    <?php if(is_home() && !is_paged()): ?>
    <div id="highlightcat2">
    	<h3 class="head">Latest SNS Updates <a title="More SNS Updates" href="https://ygladies.com/category/snsupdates">more+</a></h3>
		<?php if( $themesbyrozeh_settings['highlighted_cat2'] ) : ?>
        <?php query_posts('posts_per_page=2&cat=' . $themesbyrozeh_settings['highlighted_cat2'] ); ?>
        <?php while (have_posts()) : the_post(); ?>
        <?php
        $extra_classes = array('orange','green','blue','indigo','violet','pink','red');
        $extra_class = $extra_classes[$wp_query->current_post%count($extra_classes)];
        ?>
        <?php $do_not_duplicate[] = $post->ID; ?>
    	<div class="post ptop2 <?php echo $extra_class; ?> clearfix">
            <div class="feat">
                <?php
                // Must be inside a loop.

                if ( has_post_thumbnail() ) {
                    the_post_thumbnail();
                }
                else {
                // nothing here
                }
                ?>
                <span class="date"><?php the_time('d F y') ?></span>
            </div>
            <div class="entry">
                    <div class="entryinfo">
                        <?php edit_post_link('Edit', '<span class="edit">', '</span> -'); ?> <span class="author"><?php the_author() ?></span> - <span class="comment_count"><?php comments_popup_link('0 Comments', '1 Comment', '% Comments'); ?></span>
                        <h2><a href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></h2>
                    </div>
                    <p><?php echo limit_words(get_the_excerpt(), '30'); ?>.</p>
                    <a class="readmore" href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title(); ?>">Read More &rarr;</a>
            </div>
        </div>
        <?php endwhile; ?>
        <?php endif; ?>
        <?php wp_reset_query(); ?>
    </div>
	<?php endif;?>
    <h3 class="head">Recent Posts</h3>
    <div id="entries" class="clearfix">
		<?php query_posts(array('post__not_in'=>$do_not_duplicate));
		 if (have_posts()) : while (have_posts()) : the_post();
		 ?> 

		<?php
        $extra_classes = array('blue','indigo','violet','pink','red','orange','green');
        $extra_class = $extra_classes[$wp_query->current_post%count($extra_classes)];
        ?>

        <!-- start entry post -->
        <div class="post pfloat <?php echo $extra_class; ?>" id="post-<?php the_ID(); ?>">
            <div class="entry">
                <div class="feat">
					<?php
                    // Must be inside a loop.

                    if ( has_post_thumbnail() ) {
                        the_post_thumbnail();
                    }
                    else {
                    // nothing here
                    }
                    ?>
                    <span class="date"><?php the_time('d F y') ?></span>
                </div>
                <div class="entryinfo">
                    <?php edit_post_link('Edit', '<span class="edit">', '</span> -'); ?> <span class="author"><?php the_author() ?></span> - <span class="comment_count"><?php comments_popup_link('0 Comments', '1 Comment', '% Comments'); ?></span>
                    <h2><a href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></h2>
                </div>
                <p><?php echo limit_words(get_the_excerpt(), '30'); ?>.</p>
            </div>
        </div>
        <!-- end entry post -->

        <?php endwhile; ?>
        <?php else : ?>

        <div class="post">
            <div class="entry">
                <h2>Not Found</h2>
                Sorry, but you are looking for something that isn't here.
            </div>
        </div>

        <?php endif; ?>
        <?php wp_reset_query(); ?>
    </div>
    <div id="pagi">
        <?php previous_posts_link('&larr; Previous') ?><?php rozehtheme_pagination(); ?><?php next_posts_link('Next &rarr;') ?>
    </div>
</div>
<!-- end content -->

I thought I made it work (the classes are there and there are no duplicate posts but when I went to page/2/, it’s displaying the same posts in loop 4.

I hope anyone can help me here. I will forever be grateful. ??