Why is it that things that should be simple are not. Connecting my Window Phone to a Windows 8.1 machine to deploy my apps. So, I installed Zune (???) and the Windows Phone SDK 8.1 (it took hours) and still had errors. I ran the Windows Phone Registration tool and it consistently fails. Reboots (phone and computer) do nothing to help, nor do new/different USB cables help. There are many items out there to help.
This link:
http://stackoverflow.com/questions/24153897/getting-error-unable-to-connect-to-a-phone-make-sure-the-windows-phone-ip-over
And it leads to this link:
http://irisclasson.com/2013/10/28/problems-and-fixes-when-registering-a-windows-phone-8-device-to-deploydebug-applications/
The solution (for me) turned out that I had to manually restart the Windows Phone IP Over USB Service. It doesn't matter that you just rebooted, and it says it is running. I got "Unable to connect to a phone. Make sure the Windows Phone IP over USB transport service is running" ever time until I manually restarted it.