I had only driven one manual 240D and it was night and day over the automatic. Loved the automatics though. For an early automatic transmission to last in a heavy car for 300+K miles was pretty amazing.
What is also really amazing is the differenc e of the 240D (the 616 non turbo 4 cyl) versus the power of the 5 cyl and the turbo 5 cyl in particular as well...
So I'm still sort of confused on all of the trucks they came. I've got a pretty good jist I believe. Still if I was going thru all of that work to put it in an FJ 40/60 I'm not sure if I would go chevy or not. Like you said the t-case gearing options are good in the Toyota realm. I would also have to look about the t-case drops. Aren't most chevy's meant for a centered rear diff while the toyotas are offset?
The pickups also use a centered rear diff. The rear axle on these is pretty strong, especially the V6 diffs. I used one of these behind a 4BT with a NV4500, and the only weakness was actually the housing. I did some welding between new perches (you usually have to cut off the stock ones and weld on new ones anyway when switching vehicles, due to width changes) and added some 1/4" strap between the housing and the perches, and this worked wonders. But many people are using custom axle housings (that are also somewhat cheap)
http://www.trail-gear.com/rock-assault-axle-housing and you can use Tacoma V6 diffs with locking differentials used for usually less than $400-500 max (I paid $275 for my last one).
So these are some of the options. The Toyota pickup platform is really pretty good and unique and lots and lots of options...