If you want to better your old FJ40, which it kinda sounds like you do...
Take your donor FJ40 body. Put it on a scratch built chassis with safari diffs, coil overs etc etc so that the articulation is insane.
Engine, box and transfer case can be what ever takes your fancy. LS2 again with a supercharger?
I think the extra cost to do it this way would be worth it for the end result compared to the FJ40 body on the SWB Safari chassis. Majority of the cost is in the little things which are required for both builds anyway
Thats if your still thinking of building from scratch