Not exactly sure what this is telling me, but:
PiAware on working Pi
pi@piaware:~$ lsusb -t
/: Bus 01.Port 1: Dev 1, Class=root_hub, Driver=dwc_otg/1p, 480M
|__ Port 1: Dev 2, If 0, Class=Hub, Driver=hub/5p, 480M
|__ Port 1: Dev 3, If 0, Class=Vendor Specific Class, Driver=smsc95xx, 4 80M
|__ Port 5: Dev 4, If 0, Class=Vendor Specific Class, Driver=usbfs, 480M
pi@piaware:~$
Non-working Pi
pi@piaware:~$ lsusb -t
/: Bus 01.Port 1: Dev 1, Class=root_hub, Driver=dwc_otg/1p, 480M
|__ Port 1: Dev 2, If 0, Class=Hub, Driver=hub/5p, 480M
|__ Port 1: Dev 3, If 0, Class=Vendor Specific Class, Driver=smsc95xx, 480M
pi@piaware:~$
Hooked up to the TV with a basic Raspberry PI SD card and it powered up, but the USB keyboard and Mouse did not work.
Looking at this from a hardware standpoint I plugged in a USB to 5V barrel plug cable and took a voltage reading on the plug. The working Pi had the 5V on the barrel plug the non woorking Pi had 0V on the plug.
So, thank you for all your help. Only question remaining is: What can I use a Raspberry Pi for when the USB ports are dead?