Yes they use the same transfer case and rear diff part way through doing a conversion on mine. I don't know if the ratio for the auto box to the manual box are the same though.
As far as i know they are the same, transfer case part no. is: MR430727 (And that's goes for the PFL and FL, Manual and Auto)
And rear diff has a new part no. of : MR430996 Which is also same as PFL Manual/Auto and FL, Manual only)
But for some reason the Auto FL series 2 has a part no of : MR430727 but i think it will still work either way because MR430996 and MR430727 have the same ratio of 3.312, it might have been a small change thats why it has a different part no.
But hopefully someone can confirm it 100% regarding the series 2 Auto rear diff.