
I'd say hard pass on that idea.
While the 4.0L is a decent engine, there are other issues to deal with. I'm assuming you are talking about the AW4 automatic which is an Aisin tranny. It seems to be a decent enough tranny. The NP203 t-case behind it is centered rear output which won't work with cruiser axles. Are you thinking Jeep axles?

that is the Dana 35c that was in Cherokees? Terrible idea. Now you can update to a bigger axle but your swap is getting more and more complex.
If you are going to the trouble to swap because you want an automatic (nothing wrong with an automatic) you see most people swap to V8 or diesel. In an FJ40, you have not much room to work with for rear driveshaft. A V8 swap you can move the engine forward to get more room for rear driveshaft... not too mention much more power than a 4.0L.
I don't think you will get an inline 6 and Toyota auto in an FJ40 without moving that rear axle back a bit.