I've narrowed the problem down to this could string. This is what determines the link on the main page, that leads to a 404 not found error when trying to access the author.
<h2><a href="<?php the_permalink() ?>" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></h2>
<h3><?php the_time('F jS, Y') ?> | By <a href="author/<?php the_author() ?>"><?php the_author_meta('first_name'); ?></a></h3>
<?php the_content('Continue reading »'); ?>