Upgrading Drupal

I am trying to upgrade a Drupal/Civicspace site that I have become the admin for. I followed the upgrade directions and backed up the live site, and then copied the site to another test directory on the same server. The settings file was changed and I can connect to the duplicate db.

HOWEVER:

When I go to the home page I get 'most' of it. The top header image is missing and then any link I click I get a page not found error. It's like the engine isn't running. The live site works great, but the test site is bunk.

Here is a copy of the upgrading process from drupal 5rc1 (It's the same text for the previous versions, as far as I can tell). I've intermixed it with my comments, though the entire 'upgrade.txt' document has been reproduced.

// $Id: UPGRADE.txt,v 1.3 2006/07/10 19:27:52 dries Exp $

UPGRADING
---------

1. Backup your database and Drupal directory - especially your
sites-directory which contains your configuration file and
any added modules and themes.

This makes absolute sense and easy to follow.

As an aside, a question arises though, how is it known what the added modules and themes have been. I suppose this is more an issue after successful upgrade and probably will stand out as the themes and/or modules not there.

2. Log on as the user with user ID 1.

This is where I'm lost. Is this indicating to log into the old version of drupal (the one about to be upgraded) as the user that created it, user 1. Why? The following points or instructions, as far as I can glean, only involve the use of an FTP program to delete and upload files.

3. Remove all the old Drupal files then unpack the new Drupal
files into the directory that you run Drupal from.

If my understanding is correct, effectively delete the root drupal folder that contains all the drupal sub-folders and files. At this point, I'm at a loss as to why Point 2 above is made (logging into the old drupal site as user 1).

I am upgrading the drupal site from 4.6.3 to 4.7.4. After disabling all the non-core module, I installed the new drupal 4.7.4 base and the corresponding files (.htaccess, settings.php, etc.). However, when I call the update.php script, I continuously got the message saying "the page cannot be displayed". Any clue?

Thanks.

FYI,
After upgrading our drupal from 4.6.3 to 4.7.4 (MySQL backend) we noticed we could not subscribe users to some of our existing organic groups. The following error messages being logged to the admin log:

Unknown column 'notification' in 'field list' query: SELECT selective AS og_selective, description AS og_description, theme AS og_theme, website AS og_website, register AS og_register, directory AS og_directory, notification AS og_notification, language AS og_language FROM og WHERE nid = 275 in /home/developer/html/includes/database.mysql.inc on line 121.

My host just upgraded to PHP5.2 which has caused my drupal install to break as outlined here. I downloaded the patch and attempted to install it using the patch command in the Unix core of Mac OSX (via Terminal). However I got the following error

All users see is the "Welcome to your new Drupal powered website..." with the text that I should create my first account and so on.

When I log in I can see all my content as it was before I upgraded. I'm stumped... Iäve tried creating a new account but since I already have a "first account" this does nothing.

My site is : http://www.axbom.se/