Are you serious? First off, 40's make shitty tow vehicles- the wheelbase is to short to tow much of anything. Secondly, a 40 will out wheel a 60 anyday. Third, that 60 will weigh quite a bit more than the 40. Fourth, don't ruin a perfectly good FJ40 by stuffing a stupid 350 into it. Call me a jerk or whatever, but I think you should keep it TOYOTA. Do something original- anybody can put in a 350 in a 40.
The tranny you want is a 4 speed SM465- they've got a stupid low 1st gear that is great for crawling. For on road use, you want a H55F tranny (overseas market 5speed) in the 40. On the 60, you can just put in a later model FJ62 5speed trans.
Ryan