The 6 male pins at the edge of an Uno opposite the USB connector are designed to be the same on all Arduino boards. (The 6 male pins near the USB connector are for programming the 16U2 microprocessor and should be ignored)
Otherwise I can't think of any reason to change what I said in Reply #2.
This project is too complex to be able to specify all the requirements up front.
Be aware that a DUE works on 3.3v rather than 5v which may have implications for the things it can connect to. Also there will be many fewer Forum members with experience of the DUE.
...R