warnings after installing Multi-DB

I completed a fresh WP 3.5 multisite sub-domain install. Zero plugins installed.

I got to Step 5 of the Usage instructions, and navigated to mysite.net/wp-content/scripts/move-blogs.php

Things seemed right but it was showing only tables from my global database. (I am trying to include 4096 databases).

I clicked the link in Step 4 of the 9 instructions.

I got a number of warnings at the top of the page, then the table below seemed fine. These two warnings were repeated about 20 times:

Warning: mysql_free_result() expects parameter 1 to be resource, string given in /home/mudbug/public_html/wp-content/scripts/move-blogs.php on line 140

Warning: mysql_free_result() expects parameter 1 to be resource, string given in /home/mudbug/public_html/wp-content/scripts/move-blogs.php on line 141

I navigated to my primary site homepage, it looked as it should.

When I navigate on the front and back-end of the site, I'm getting warnings at the top of the page such as:

Warning: mysql_set_charset() expects parameter 2 to be resource, boolean given in /home/mudbug/public_html/wp-includes/wp-db.php on line 650

Warning: Cannot modify header information - headers already sent by (output started at /home/mudbug/public_html/wp-includes/wp-db.php:650) in /home/mudbug/public_html/wp-includes/pluggable.php on line 876

I tried to create a new site, it's not working but it is showing-up in my Network sites.

Your help would be much appreciated!

Andy