I made some more progress. I reviewed the circuit and I had the BB-AR pins reversed. I was going TX-TX and RX-RX. I verfied they are now routed correctly. I also had a bad resistor that needed to be replaced. Finally I switched to using UART2 instead of UART1. My thought was that I may have burned out UART1 by sending in a too much voltage. If I manage to get it working on UART2 it should be simple to move back to UART1. For now I think I am going to either pick up a Arduino board and use that via USB until I can figure out how to make the connection between the two and when I do I can swap the chip from the Arduino to my breadboard and verify the chip I have actually has a bootloader.