BTW -the front on a Sahara and X models is a D30, not a D35...and, they significantly upgraded the D30 on the JK's, so it is as strong as the old front D44.
That aid, they ALSO upgraded both D44's on the JK too, so they are a lot stronger than the old D44's...but the front D44 is still using the new D30 ends.
The automatic is geared more towards the overdrive end than the manual (0.69 auto vs 0.84 for the 6th gear...), and the STOCK gearing is 3.21 in the diffs, with 3.73 optional for $50, or part of the tow package....but the Rubi comes with a torquier 4.10 diff set...and the 4:1 T-Case vs a 2.72 T-case in the others.
If planning to wheel it, throw on 35's...but not swap drivetrain parts, etc...go with the Rubi Unlimited...as its long enough to be higher tow rated, has the room you need, and can handle 37's if need be, etc.
As for manual or auto...the 6 speed will be peppier, the auto is the easy button.