There are lots of good transmission options and advice posted above. All of the transmissions above can work fine... but... use that gear calculator and don't guess or you may be doing it twice:
Use the gear calculator to figure out how to hit the ideal engine RPM at cruise with your 401. If you want to cruise at 65 mph and get the best possible mileage and power response-- then target your gearing and tire combo to put the engine at the RPM that produces peak torque when you are cruising at 65 in top gear. If you want to cruise at 55mph on back roads more, then figure for that (or 60) instead.
Then figure out an acceptable off-road crawl ratio range, and take tgreese excellent post above into consideration. Since you are talking about an automatic transmission, gearing doesn't need to be as low as with a manual. Figure on a crawl ratio from 30 to 1 to the 60 to 1 range. Play with the available transmissions, t-cases and axle ratios to get matches that will be in the ballpark for cruising and for off-road. If you get the ratio's on the axle and transmission wrong-- it won't work optimally regardless of what axle, case or transmission you run. Your engine or transmission (or both) may overheat. Your fuel economy will likely stink (well, it is a 401-- so it ain't ever gonna be great) and even with the mighty 401 your Jeep will feel sluggish at times or your engine will be revving itself to death. It would be an expensive mistake to guess here and have to redo it or live with it.
I debated telling you this, since it isn't what you asked for advice about.. but:
A Dana 60 and an Atlas seems like lots of coin to spend on something that isn't "a serious offroader". There are lots of cheaper tough and durable options in the transfer case department if you don't need the steep low gearing or stupid tough competition level case (admittedly, I have not checked prices on used cases lately though). If you aren't planning on running 37 inch or larger tires, you probably don't need the Dana 60 either. It is lots of weight and less ground clearance over smaller options, which is critical on 35 inch and smaller tires. The cheapest option is to beef the stock axle. There is usually nothing wrong with a beefed Dana 44 or AMC on 35 inch or smaller diameter tires. Then there are other lighter custom options, something like a Currie full float conversion on a Ford 9 or a new built 44. Much more pricey, but so is building a 60 typically.