also, because of differences in the SQL engine's optimizer between versions, if you upgrade from 2005 to 2008R2 like you said, at a minimum you need to updating statistics, and i'd consider rebuilding the indexes , as that is a critical piece that must be part of your upgrade process.
you can search and there's lots of posts stating "new server is slower than old one", and that is often a root cause.
DECLARE @Exec VARCHAR(MAX)
SELECT @Exec = ''
SELECT @Exec = 'UPDATE STATISTICS ' + QUOTENAME(schema_name(schema_id))+ '.' + quotename(name) + ' WITH FULLSCAN ; ' + CHAR(13) + CHAR(10) + @Exec FROM sys.tables ORDER BY name DESC
PRINT LEN(@Exec)
PRINT @Exec
EXEC(@Exec)
Lowell