Upgrading Drupal

In phpmyadmin, whenever I select all the tables in my drupal database and perform a "Check table" on them, the whole list usually returns with Status OK, but at the bottom of the page I get a pile of error/warnings:

I upgraded from 4.5.2 to 4.6.1 and cannot find the sub-links below admin->logs->

error
regular
search
special
user
hits
referrers

where are they?

I upgraded my site from 4.6.0 to 4.6.1 by copying the files from the 4.6.1 tar file to my directory structure, replacing the settings.php file with my backup copy, then running the update.php script to update the database. Whenever I try to navigate to the home page of the site I get the following:

Fatal error: Call to undefined function drupal_add_link() in /home/username/public_html/modules/blogapi.module on line 533

As far as I can tell I've upgraded from 4.5.2 to 4.6.1 successfully, however, when I try to search the same string in the 4.6.1 version nothing is found but many entries are found for 4.5.2. Yes I did copy all the content of 4.5.2 to 4.6.1.

Interestingly the paths are different for when search is clicked in my theme for the two versions.

4.6.1: ?q=search/node

4.5.1: ?q=search

Help!!!

I've been having this problem since upgrading from 4.5 then to 4.6.0, and the issue seems to persist into 4.6.1.

When the cron run is happening, it is returning the following error(s)

I am struggling mightily to upgrade from 4.5 to 4.6. I must be missing something in transferring the data from the old database to the new version.

From http://drupal.org/INSTALL.txt, I read that I should "remove all old Drupal files then unpack the new Drupal files into the directory..."

So I overwrote /database/database.mysql and /database/database.pgsql (after first copying the files to my PC and dumping the database).