Most probably you need to create a front-page.php because index.php should be used as failback for other templates or when the home page contain a stream of last posts, in your case, use front-page.php is better.
After that, choose post or pages depens on the content, but being a WP theme, most probably user already have posts or want to add posts (for news, blog sections, and so on) so if your theme do not handle posts at all I think it's not a great choice.
Just for example, the "Book review videos" section can be filled using post-format video and category "review" (or using a CPT "review")... "Chapters" section can be filled using a CPT "chapters"... "Messages from readers" section can be filled using a CPT "messages"... and so on.
These are only examples, stop some minutes and think about the structure, considering that your theme will be used by people that may already have content, and that in some cases want switch from your theme to another, try to make this passages more easy as you can.
Also consider that specific CPT will be easier for users understand how add content for various sections. Only when you are sure create it.
Note that if you use posts (standard or CPT) you can make use of taxonomies (categories, tags or custom), and post format that will help you a lot to select post for the various section.
If you use pages, to select which page goes in a section and which in another, you have to create some theme settings or force users to call their pages with specific title... it's not a great idea.
(If you create a custom taxonomy you can assign it to pages, but WordPress users are familiar with taxonomies for posts, not for pages, and then post format are availble only for posts).
After that, pages are just posts with post type setted to page, you can query just like any other post type:
$args = array(
'post_type' => 'page',
'posts_per_page' => 2,
'post_parent' => 0,
'order_by' => 'title',
'order' => 'ASC'
);
$query_for_two_parent_page = new WP_Query($args);
Exist also the function get_pages that is similar to get_posts but saves you to type 'post_type' => 'page' in the arguments.
As final note, instead of loading all the content when fron page load: think about load the content using ajax when content it's requested: e.g. when the related section is reached scrolling the page or e.g. for "Chapters" section load the requested chapter when the related link is clicked...
