I think you need to do two things here:
1. EPiServer Deployment Center connects to the database using your current windows credentials. Make sure your windows user has sufficient rights in the database.
2. Start over with a fresh copy of the database. It seems to have been corrupt in your first attempt to upgrade.
I am trying to upgrade the site to version 6 R1, and have some issues. First of all my site and database are on two different machines. The database version is "Microsoft SQL Server 2008 R2 (SP2) - 10.50.4000.0 (X64) Jun 28 2012 08:36:30 Copyright (c) Microsoft Corporation Developer Edition (64-bit) on Windows NT 6.1 <X64> (Build 7601: Service Pack 1) (Hypervisor)"
1- Time out issue on executing sql server and it stops on "exec dbo.netCreatePage". I commented this line to run it later after upgradtion but later on got the following message?
2- Error - Dynamic Data Store 6.0.318.113 can only be used with database version 6001, current version is 6204. Make sure both database and assemblies are upgraded correctly.
Please note, I have done one upgrade earlier, but was different version of the database.
You help is much appreciated.