Hi Neil,
We mux the peripherals to multiple pins to enable a wide range of configurations (i.e. we have more capability on-chip than pins allow so we mux and let you choose what pins to have the peripheral capability come out on).
Now you cannot have the UART3 connected to more than one set of pins simultaneously. Yes you could dynamically change this. It just is not a typical application.
You need to be sure other application code is not trying to use those pins as well (i.e. avoid contention).
Once you have played around, feel free to post your project.
Are you using the freedom or tower hardware for development? If yes, that makes life much easier for us to help support.
Please note I looked at the reference manual for the 100-pin and see a difference:
UART_TX/RX on pins 5&6....not 6&7.
Regards,
David