As I mentioned **I was going to be start working on this need immediately** so I'm making headway. Given that I'm knocking these down I figured it's best to start posting them. *Still, if someone else can/will post (some of) the parts I haven't done I'll be happy to let you copy whatever I'd done you haven't and select your answer as the best answer.* Until then I'm going to start posting the code.

## First Thing: Include `wp-load.php`:
Since we're creating a standalone file in the root of the website to run initialization that will only be used to "bootstrap" a site *(I called mine `/my-init.php`)* we start by including `/wp-load.php` to load the WordPress API functions:

    <?php
    include "wp-load.php";

## Creating Users for the Site
We'll use the `wp_insert_user()` function located in `/wp-includes/registration.php` to create our users. This file is not loaded by default so we'll have to load it ourselves with a call to `require_once()`. 

We'll also use the `get_user_by()` function to first see if the user has already been created; no need to run the code twice if they haven't. ***NOTE:** This is a pattern will follow; e.g. our script should not duplicate or overwrite anything if called multiple times, especially after users have added or changed data for any of the items we plan to initialize.*

    require_once( ABSPATH . WPINC . '/registration.php');     
    $user = get_user_by('slug','johnsmith');
    if (!is_object($user)) {
      wp_insert_user(array(
        'user_login'        => 'johnsmith',
        'role'              => 'administrator',
        'user_email'        => '[email protected]',
        'user_url'          => 'http://example.com',
        'first_name'        => 'John',
        'last_name'         => 'Smith',
        'comment_shortcuts' => '',
        'use_ssl'           => '0',
        'user_pass'         => '12345',
      ));
    }

##Deleting the *"Hello Dolly"* Plugin
To delete the *"Hello Dolly"* plugin *([sorry Matt][1])* we'll use the `delete_plugins()` function. `delete_plugins()` expects an array of file paths that are relative to the `/wp-content/includes/` directory. For the *Hello Dolly* plugin the file path is simply `hello.php` since the *Hello Dolly* plugin isn't stored in it's own directory but for most plugins it will be in the form of `{$subdir}\{$filename}.php`; i.e. the file path for Akismet is `akismet/akismet.php`.

However, `delete_plugins()` is not available until we've included `/wp-admin/includes/plugin.php` and there's also a dependency with `wp-admin/includes/file.php` so we `require_once()` both of those before we call `delete_plugins()`. Finally we use `WP_PLUGIN_DIR` constant combined with `file_exists()` to see if the main plugin file exists before we attempt to delete it *(not that is would matter if we tried to delete a missing file, but it's more elegant to actually check first and you might need to know how for some other reason)*:

    require_once(ABSPATH . 'wp-admin/includes/plugin.php');
    require_once(ABSPATH . 'wp-admin/includes/file.php');
    if (file_exists(WP_PLUGIN_DIR . '/hello.php'))
      delete_plugins(array('hello.php'));

*Note* that sometimes `delete_plugins()` will fail because of file permissions or maybe the fact a plugin is currently activated or some other reason that you'll first need to resolve but for our use-case *Hello Dolly* goes away without a fight.

##Downloading, Installing and Activating Repository Plugins
I don't actually need to download plugins from the repository right now *(I was thinking it would just be a nice to have)* we're going to let this requirement slide and revisit it later.

##Activating Your Plugins
Next up is activating our own custom plugins. We are assuming we have already uploaded them to the plugin directory and all we need to do it *activate* them for WordPress. *(**Note**: This technique will work for activating repository plugins too, it just won't download and install them first.)*

We'll use the `activate_plugin()` function which like `delete_plugins()` requires `/wp-admin/includes/plugin.php` to be included but *does not* need `/wp-admin/includes/file.php` in case you are only needing to automate activation and not deletion. 

We'll again test for existence *(not need to activate if not there, eh?)* and we'll also verify using the `is_plugin_active()` function that the plugin has not already been activated. Note I used a few variables this time (`$plugin_filepath` and `$plugin_dir`) to keep from duplicating the plugin identifier numerous times. 

Our example that follows activates the plugin `my-custom-plugin.php` which is located in the `my-custom-plugin` subdirectory:

    require_once(ABSPATH . 'wp-admin/includes/plugin.php');
    $plugin_filepath = 'my-custom-plugin/my-custom-plugin.php';
    $plugin_dir = WP_PLUGIN_DIR . "/{$plugin_filepath}";
    if (file_exists($plugin_dir) && !is_plugin_active($plugin_filepath))
      activate_plugin($plugin_filepath);

##Activating Your Preferred Theme 
Activating a theme is a bit easier than deleting or activating a plugin, comparatively speaking; one function call is all that is required: `switch_theme()`. The `switch_theme()` function accepts two *(2)* parameters: the ***template*** and the ***stylesheet***. Well, at least that's what the parameters are named. You might be more familiar with the terms [***Parent Theme*** and ***Child Theme***][2].

Assuming you've created a *Child Theme* with the default TwentyTen theme that comes with WordPress being the *Parent Theme* and you called it *"My Custom Theme"* and placed it into the `/wp-content/themes/my-custom-theme` directory, you'd activate your theme using this call:

    switch_theme('twentyten', 'my-custom-theme');

But what if it is not a child theme? That's easy, just pass the **directory slug/theme identifier** *(i.e. the name of subdirectory off of `/wp-content/themes` that contains your theme)* as both parameters.  Assuming you want to activate the [Thematic theme][3] by [Ian D Stewart][4] you've call `switch_theme()` like so:

    switch_theme('thematic', 'thematic');

Personally I think it's a bit whacky to have to keep track of both details here so I wrote a function called `activate_my_theme()` that first checks to make sure the the `get_current_theme()` function and if not activates it. You just need to tell it the child theme *(aka the "stylesheet")* and it figures out the parent theme for you *(aka the "template")* by grabbing the details from the `get_theme()` function. 

    activate_my_theme('My Current Theme');
    function activate_my_theme($theme_name) {
      if ($theme_name!=get_current_theme()) {
        $theme = get_theme($theme_name);
        switch_theme(
          $theme['Template'],
          $theme['Stylesheet']
        );
      }
    }

**One key point to be aware of**; the `get_theme()` function expects to be passed the ***name*** of the Child Theme, *NOT* it's directory slug/theme identifier. *(The name comes from the "Theme Name:" section in the header of the theme's `style.css` file. Fortunately the `get_current_theme()` function returns the name too.)*  

Inspecting the header in the `style.css` file of the WordPress default theme *Twenty Ten* we see it's name is in fact `'Twenty Ten'`:

    /*
    Theme Name: Twenty Ten
    Theme URI: http://wordpress.org/
    Description: The 2010 theme for WordPress is stylish, customizable, simple, and readable -- make it yours with a custom menu, header image, and background. Twenty Ten supports six widgetized areas (two in the sidebar, four in the footer) and featured images (thumbnails for gallery posts and custom header images for posts and pages). It includes stylesheets for print and the admin Visual Editor, special styles for posts in the "Asides" and "Gallery" categories, and has an optional one-column page template that removes the sidebar.
    Author: the WordPress team
    Version: 1.1
    Tags: black, blue, white, two-columns, fixed-width, custom-header, custom-background, threaded-comments, sticky-post, translation-ready, microformats, rtl-language-support, editor-style
    */

##Deleting the *"Hello World"* Post
Next we want to delete the *"Hello World"* post. You may have seen that *@Rarst* has shown us how to use the `wp_delete_post()` function which is exactly what we need. As he explained the second parameter will fully delete the post as opposed to moving it to the trash and the first parameter is the `$post->ID`. 

Of course it would be nice to be able to specify [**the slug**][5] instead of the `$post->ID` and so I decide to find a way to do that. After some spelunking I found that WordPress has an unfortunately named function called `get_page_by_path()` which actually allows us to look up any post type by its slug *(it is unfortunately named because you might overlook it when trying to find something that works with post types other than `'page'`.)* 

Since we passing  `get_page_by_path()` the WordPress-defined constant `OBJECT` it will return to us a post in the form of an post object. For the third parameter we passed `'post'` to indicate we wanted it to lookup post types of `'post'`. Since `get_page_by_path()` will return the post object we need or return `null` if no post matches the slug we can check for existence and do a lookup at the same time:

    $post = get_page_by_path('hello-world',OBJECT,'post');
    if ($post)
      wp_delete_post($post->ID,true);

*Note:* We could have run code to delete every post in the database but if we had we would not be able to run this code again once we've added the posts we want to keep and that was one of our design constraints.

##Next...
I'll keep adding to this as I figure it out until I'm done or until someone else helps out.


  [1]: http://books.google.com/books?id=sXZiavO78M4C&pg=PA213&lpg=PA213&dq=matt+mullenweg+hello+dolly&source=bl&ots=Zj62cP_fVM&sig=cydmzUpwGEIevB4kEjNUkSgxCcA&hl=en&ei=HZ6NTIHIMsKqlAeMyYFj&sa=X&oi=book_result&ct=result&resnum=2&ved=0CBcQ6AEwAQ#v=onepage&q=matt%20mullenweg%20hello%20dolly&f=false
  [2]: http://wordpress.stackexchange.com/questions/290/#291
  [3]: http://wordpress.org/extend/themes/thematic
  [4]: http://themeshaper.com/about/
  [5]: http://codex.wordpress.org/Glossary#Slug