Server 2012 Linked Server From An Instance
Comments were very useful in leading to the solution.  After running SQL Server Kerberos Configuration Manager I saw that while the first was on 1433 for SiteADefaultInstance and the second instance of the database was listening on a dynamic port for SiteASecondInstance.  

Went into SQL Server Configuration Manager > SQL Server Network Configuration > Protocols for SiteASecondInstance > TCP/IP and change IPALL TcpPort to a different port, say 9999.

SetSPN -s "MSSQLSvc/SiteAServer:9999" "user"


After this could create a linked server.