I am surprised to learn that the AT91SAM7S-EK eval board does not bring out all three UARTs. It seems like such a basic functionality would be provided. This is especially surpising when I found out that there is an unused transmitter and receiver in one of the RS-232 chips!
I need all three ports, so I am going to wire up UART1 to the unused IOs and bring it out to the same connector as the debug port. If anyone is interested I can provide the info on how to make the change. It looks like it will require one via drilled since it is under the IC and one trace cut with four jumper wires.
Pretty simple... but I have not done it yet, so I'll wait until I have tested it before I post it.