If you check HAL.cpp in the development tree you see
#if defined(UBRRH) && defined(UBRRL)
RFHardwareSerial RFSerial(&rx_buffer, &tx_buffer, &UBRRH, &UBRRL, &UCSRA, &UCSRB, &UDR, RXEN, TXEN, RXCIE, UDRIE, U2X);
#elif defined(UBRR0H) && defined(UBRR0L)
RFHardwareSerial RFSerial(&rx_buffer, &tx_buffer, &UBRR0H, &UBRR0L, &UCSR0A, &UCSR0B, &UDR0, RXEN0, TXEN0, RXCIE0, UDRIE0, U2X0);
which initializes the serial connection. It is hardwired to use RX0/TX0. I do not know if the serial Port connector uses a different serial interface, but I would guess so. So you need to find out which and change the registers to use that port. If it is a mega compatible, which I think it is, you need to change the second version and replace the 0 with 1-4 depending on the connection you use.
Function will be completele identical, but you will lose the reset on connect capability you have over usb.
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