once i have the upgrade package i will let you know how that goes, but to let you know i have a back end way of doing it. My way is:

Open upgrade.php Take out the mysql updates and goto my adminmysql and run them from there, then what is is left in the upgrade.php file i run from the file.

Reason for this is becuase when ever i run the upgrade.php i always get a database error. The way i do it there is no errors at all. :)