Also, This is the way I run all of my SQL Instances and I don't have any problems with login issues. It may or may not be correct but it works well for me.

1. Enable TCP/IP Client protocol only. (Disable the rest)

--Change Port number

2. Alias the Instance name with the new port number. (This is the key)

3. Setup Alias on the agent so I can join my MSX/TSX Correctly.

4. When I create a linked server I use with trusted connections.

--Always make sure I alias the remote machine.

5. I always use AD Accounts/Groups to contorl my security. I never assign a local and/or group/AD Account security to remote login.