I came accross a couple of problems whilst upgrading a site which uses Multi Site Manager and quite a few AddOns so I thought I would share some of the things which I needed to do in order to get the upgrade working.
I discovered that it was necessary to upgrade all the AddOns, Modules, Extentions etc before I began. This is because some of them will cause a fatal error after the upgrade and prevent you accessing the control panel.
The installation didn't quite complete correctly, I was left with an empty box instead of the instructions to remove the install folder; not a great place to be. So I had to finish of the installation manually. Incidentally @johndwells suggested removing a survey from the installer: "Try removing views/surveys/survey_290.php from installer and re-running… If it works, we should compare notes!". Maybe this will work for you, if not read on.
To complete the installation I needed to add some columns to the database and try installing again.
For the exp_template_groups table I needed to add an order column. Here is the SQL statement:
I hope that this post may be useful to you.