How do you use PORTD on Leonardo with a Mux?

I am looking at the AT Mega chip for Leonardo (Arduino - PinMapping32u4) and if I wanted to hookup a multiplexer to, say, Digital Pins 0 1 2 3, how do I cycle these ports in order when:

PD0 = Pin 3
PD1 = Pin 2
PD2 = Pin 0
PD3 = Pin 1

I have only used PORTB before, and PB0-3 corresponds directly to 8 - 11, in order.

Do I simply just hookup the multiplexer selectors in a different order? So 'S0' goes to Pin 3, 'S1' to Pin 2, and so forth.

Do I simply just hookup the multiplexer selectors in a different order?

That will work. Since the pins are in sort-of-random order, you can either fix this in hardware by re-wiring as you describe, or you can fix it in software by mapping your mux selection to different values:

byte portDpermute[16] = { 0b0000, 0b0010, 0b0001, 0b0100m, ... };
PORTD = (PORTD&0xF) | portDpermute[val];