If you are doing an in-place or side by side upgrade, ensure (as in, make it impossible) that no one is accessing the v2 site while the install/upgrade is happening.

Here is an example of one of the problems you may encounter if users access the site during upgrade.

http://support.microsoft.com/default.aspx/kb/928830

I have also struck problems with the embedded database upgrade if you don't leave a period of inactivity between the last site access and the upgrade (at least 10 minutes)