ifelse

To exclude the categories from being displayed in the sidebar list, you can use:
<?php wp_list_cats('exclude=1,2'); ?>
where 1 and 2 are the category_id’s for Journey or Thoughts.

Hiding it from the post categories (I assume you mean hiding from the list of categories that is shown on the right when people are posting) is a bit more difficult and will require modification to the base WP files however.

Is this what you’re looking for?

Quick note: Bumping is actually counter-productive if there have been no replies. The titles of posts with no replies are in bold which helps them stand out. Bumping a post will remove this emphasis and make it that much less likely to receive a reply.

Try downloading the gespaa_v2.zip and then uploading the single.php file to your theme directory.

You can try this;

on the first loop, do as you would normally. On the second loop however, you create a new WP_Query object (which is what handles the actions and properties for the_loop) via:
<?php $sub_query = new WP_Query('category_name=site&showposts=5'); ?>

Now you can loop through this wp_query object as you would normally:
<?php while ($sub_query->have_posts()) : $sub_query->the_post(); ?>
<?php
the_excerpt();
?>
<?php endwhile; ?>

It’s difficult to properly recommend a solution without knowing
a) how you plan to manage user/password lists
b) how your own tables are defined

If the table tables are broadly similar i.e. similar datatypes and columns, you may be able to get away with using MySQL views (whether this is a view on the WP tables or your own tables is a judgement call). However, I wouldn’t recommend this approach at all.

A better solution (besides rewriting the code) may be to write a data migration scripts i.e. some SQL/code that maps WP user tables to your own data tables (or vice versa). Just my 2 pence.

Unfortunatly, I don’t really see a perfect solution with the info provided.

There are references to localhost in your css instead of the actual blog url