It seems that the upgrade process has broken the backend templates of the website and the menu ID's have been mixed. Can you to login by going to /Sitefinity/Pages for example. From there go to Administration -> Backend pages and edit the dashboard page. Try editing the backend template by going to /Sitefinity/Template/f669d9a7-009d-4d83-cccc-000000000001
then edit the ID's of the header and the footer controls.
If you wonder what ID's can be work for you, just create a new project navigate to the above mentioned address and take the IDs.
However the best option to upgrade ( if you use 4.0 ) is through 4.1 then 4.2, because there are many changes throughout the versions which depend on each other, therefore skipping a version might lead to other issues in future.
the Telerik team
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