ikaring

You can override css like:

.page-template-template-blog img.thumbnail {
width: 100px;
height: 100px;
}

Since body tag of the blog page has following classes, you can specify css rules only for blog template as above.
page page-id-152 page-template page-template-template-blog page-template-template-blog-php safari alt-style-default one-col width-960 one-col-960 full-width full-header full-footer full-slider

Have you checked Appearance -> Customize?
There might be those settings.

It seems some javascript changes the url of youtube.
In HTML source, it’s https://www.youtube.com/sespider, but rendered url is https://www.youtube.com/embed/sespider.

YouTube Channel plugin looks suspicious to me. Pls try disable this plugin or change some settings of it.

I think your link url should be following.
https://www.youtube.com/watch?v=fSoSipSFPGA&list=PLn9N9jhgkJ3L6Ud_4FSZcb-xSoExmiUIe&index=1
or
https://www.youtube.com/playlist?list=PLn9N9jhgkJ3L6Ud_4FSZcb-xSoExmiUIe

To open link in a new tab/window:
On right top in menu settings page, there should be “Display Option” button or somekind ( I don’t know english label cos I use Japanese ).
Click that and panel expands. Check “Link target” ( I guess.. ).
Now there is a checkbox in your YOUTUBE menu item section.

BTW, nice drawings!

In that case, it is better using shortcode. Add the following code to functions.php of the theme.

function my_rb_js_handler($atts, $content=null) {
$str=<<<eot
<script type="text/javascript" src="http://www.redbubble.com/assets/external_portfolio.js"></script>
<script id="rb-xzfcxvzx" type="text/javascript">new RBExternalPortfolio('www.redbubble.com', 'sespider', 3, 3).renderIframe();</script>
eot;
	return $str;
}
add_shortcode('rb', 'my_rb_js_handler');

You can put [rb] anywhere in section and that’s it.

Why I recommend child theme is that above shortcode in functions.php will be deleted after theme update.
Child theme setup is not that difficult, so read the codex and just put above code in functions.php of the child theme.
http://codex.wordpress.org/Child_Themes

About main nav bar:
You can add menu items only after sections links. In menu settings page, select your menu and check theme location as Home Page Header Menu.

If you pass multiple categories, you should set array as the parameter.
<?php if ( in_category( array( 5,14 ) ) ) { ?>

Also, post_is_in_descendant_category function accepts only array as first parameter.