If I understand right, you have Site 1 on Server 1 and created Site 2 on Server 1. Then you created a copy of Site 1 & 2 database and code and moved them to Server 2. Is this right?
Have you checked the Kentico event logs using SQL Server query?
SELECT TOP 100 *
ORDER BY EventTime DESC
Have you checked the servers event log? How about the IIS event log?
Have you checked your websites app pool? Is it set to .NET 4.0?
Do you have any custom code specific so Site 1?
Any specific web.config settings causing the error?