These aren’t, like, options you can set. You have to edit the style.css file to change the way things look and sizes of things. To change the actual content and ordering of the content you have to open the corresponding .php file and edit the HTML. So you have to figure out HTML and CSS.
Colours in the .css file are set using hex colour notation. It can be a funny system to get used to. This seems to be a site where you can pick your colour and be told the version you need (in the format #028453, where the numbers can be anything from 0 – 9 or a – f). Then replace all references to the light blue colour (#CCCCEE) with the colour code you want.
To change header size, you have to add some width rules to the #header element. http://www.w3schools.com/css/ is a great guide.
To eliminate the hot tags, open the file front-page.php with a plaintext editor (such as Notepad) and remove a section similar to this:
<div id="hottags">
<h2><?php _e('Hot Tags'); ?></h2>
<p class="frontpageheatmap"><?php tag_heat_map(); ?>
</div>
Those are the things you asked about. For everything else I suggest you do it the hard way, by yourself, learning off the internet. Because if you have a problem and you can fix it, well, you no longer have a problem. But if you’ve got a problem and you don’t know how to fix it you might have that problem for a long time. Also Firebug is the most helpful thing you could possibly have; it lets you make changes (not permanent) to the CSS that you can instanly see and you can look at the HTML very nicely too.
Thank you fel! That’s amazing!
