Messed Up My Directory

What version of WP is it?
If it is old, your best bet is to install an up to date WP. You could save the theme you have, if it is not out-dated, by downloading its directory to your computer.
Also, drop the entire database you used, first, before installing latest WP.

I just updated it this morning. Current version is WordPress 3.4.1.
I think I messed it up inadvertently but have gotten side tracked for too many months now and cant remember how I got here, let alone how to fix it. Using Rapidweaver and placing the code so that the WP site works within my site the way I want it to. Cant remember if the key pieces are in place or not. It used to work so I am sure I did something I should not have at one point. Here is my WP directory list currently on my server:

wp-rdf.php
wp-rss.php
wp-atom.php
wp-rss2.php
wp-commentsrss2.php
wp-feed.php
wp-blog-header.php
wp-register.php
index.php
wp-pass.php
wp-app.php
wp-links-opml.php
wp-load.php
wp-cron.php
xmlrpc.php
wp-config-sample.php
wp-config.php
wp-comments-post.php
wp-trackback.php
wp-activate.php
wp-mail.php
readme.html
wp-settings.php
index.html
wp-signup.php
license.txt
wp-login.php
wp-includes
wp-content
wp-admin

Thanks

If you go to the site link you provided, there is a constantly rotating, flashing google ad there. This your problem? Remove your google ad client and see if this helps.

I am republishing the container page now. Should take a few minutes to finish and upload. All it has though, is the following code (aside from it’s css properties. This revised page has no Google ad code.

<?php
/**
* Front to the WordPress application. This file doesn’t do anything, but loads
* wp-blog-header.php which does and tells WordPress to load the theme.
*
* @package WordPress
*/

/**
* Tells WordPress to load the WordPress theme and output it.
*
* @var bool
*/
define(‘WP_USE_THEMES’, true);

/** Loads the WordPress Environment and Template */
require(‘./wp-blog-header.php’);
?>

https://thegoldenthread.net/wordpress/index.php

Now refreshed. Still showing a blank (css loaded with the basics) page.
Still no results I can use.

In your Main Theme Template, it should have (index.php) underneath it, is the any cade after the call for the header?

The fundamental loop should look like this:

<?php
get_header();
if (have_posts()) :
   while (have_posts()) :
      the_post();
      the_content();
   endwhile;
endif;
get_sidebar();
get_footer();
?>

edit: and, do you have any posts?

Simple question: The following data is what loads for my WP page withing my css wrapper in Rapidweaver. Am I reading this wrong? I could make the page point to a particular file address on my server? Is the following suggested code what it should be reading, or the file it’s self?

Thanks

<?php
/**
* Front to the WordPress application. This file doesn’t do anything, but loads
* wp-blog-header.php which does and tells WordPress to load the theme.
*
* @package WordPress
*/

/**
* Tells WordPress to load the WordPress theme and output it.
*
* @var bool
*/
define(‘WP_USE_THEMES’, true);

/** Loads the WordPress Environment and Template */
require(‘./wp-blog-header.php’);
?>

That is the index.php for WP which just tells what to load.

What you need is the index.php to your theme, which you will find in Appearance > Editor – look for the file which has (index.php) under it. It is probably Main Index Template or something like that.