Hi,
Using a Arduino Pro Mini, I've connected RXD and TXD as normal I/O pins. However, the IDE returns an error on:
pinmode(RXD, OUTPUT);
pinmode(TXD, OUTPUT);
This seems no problem for the other preprogrammed pins....
Note that having something connected to pins 0 and 1 may interfere with the ability to upload code to the board and, of course, you will not be able to use the Serial monitor for data input or output
"Do you actually need to use pins 0 and 1 for that purpose ?"
No, but those lines are the closest to the circuit they need to be used for. That is the most interesting for EMC as they will hold frequency signals.
"Have you used all of the other digital pins on the board and if so, what for ?"
Almost all, they're used to control a stepper driver and to read some buttons.
The system works just fine using the TXD and RXD as regular port lines. I can even still use the Serial commands but cannot use them then as port lines of course. This because the connected circuit lines are input only.