with a manual its easier and you have tons more useable gearing choices you can choose low low and 5th gear, with a auto your pretty much stuck with low low and 1st gear so on and so forth. Its easier to go duals with a manual trans also from what I've read and heard.
That USED to be true but it isn't any more.
You can mix and match a LOT of parts to use a LOT of different combination's if you know what you're dealing with.
Best advice to stay all toyota is to dump the a340h for a a340f out of a later rig and swap the a340h bellhousing onto it so it'll bolt to your engine. Now just toss a Marlin V6 adapter plate on the back of it and you have a perfect place to bolt geared duals.
Want to get front dig with no overpriced garbage rear disconnect? Get an AW4 out of a cherokee, bolt the a340 bellhousing and oil pan onto it then chop the 231 apart and bolt a box 4 rocks adapter onto it and run a dana 300 like I did.