I just updated one of my sites (finally) from version 3.4.4 to 3.4.9 by downloading the current version zip file, uploading to my server and then switching themes. (zero problems so far)
I noticed there is still a line of previous code in the header.php file to add the canonical tag to pages and posts. Just to let you know, there is no need for this (as far as I can tell) since wordpress version 2.9, as it has been added to the wordpress core. Might as well take it out in the next upgrade.