There seems to be a connection problem between LogStash and your MS SQL server:
Error: Java::ComMicrosoftSqlserverJdbc::SQLServerException: The connection to the host localhost, named instance desktop-l1ir1is\kibanatest failed. Error: "java.net.SocketTimeoutException: Receive timed out". Verify the server and instance names and check that no firewall is blocking UDP traffic to port 1434. For SQL Server 2005 or later, verify that the SQL Server Browser Service is running on the host.
Did you already check that the mentioned port 1434 and the instance name is correct and that the SQL server browser service is running?
Maybe someone with MS SQL Server experience can help you here as I am only using Oracle.