Help wanted on theme…

I created a theme, to fit the blog perfectly into my already existing website. I used thewordpress theme generator by Yvo Schaap.

However there are a few hickups.
Firstly, the menu (home, news, diary and so on…) has a white line above it on all other pages of the site, and here it is gone for some strange reason.

Also the table with the three blue sections starts at the top of the page, as all the other pages have a little brown spacing between the top of the blue row and the end of your browser window.

When I remove the php code in the page this problem dissolves automatically.

This is the site http://www.fortherestless.com/news.php

That code to show the blog is this btw

<?php
/* Short and sweet */
define('WP_USE_THEMES', true);
require('c:\\domains\\fortherestless.com\\wwwroot\\forms\\newz\\wp-blog-header.php');
?>

Now, what I am trying to change, is only removing the excess…

* The complete links section should be removed,
* the links for Home,sample page and uncategorized should be removed
* the “newz Just another WordPress site” bit should be gone too
* and if possible the “Filed under: Uncategorized | Comment (1)”too,
* the clickability of the title of a post should be gone too.
There is no need or desire to have anyone click on the title of the post.

Also, since news is not updated that much, I’d like to have the archive to be anually instead of monthly.
Instead of June 2011, just 2011, 2010…

thanks in advance,
I uploaded the scheme here on my site
http://www.fortherestless.com/theme.zip