Migrating data in SQL Server from source to target with schema change at target
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Copied all the data to SQL2008
Updated the schema on SQL2008 according to the upgrade script?


Copy data shouln't be the problem here, schema compare neither ;)

For the scheme compare from sql 2005 to 2008 you may use the free Open DbDiff from http://opendbiff.codeplex.com and apply the resulting script to sql 2008.

Otherwise use the new version of the SQL Server Data Tools http://msdn.microsoft.com/en-us/data/tools.aspx that allows SQL 2005 to 2008/2012/Azure migration and scheme update out of Visual Studio 2010+