I have decided to go the route of running the stock A341E trans with my 1UZ.
To properly mate the A341E to the Prado T-Case the rear output shaft had to be swapped. Since the Prado only has a 2 prong pick up for the speed sensor that had to be removed from the prado output shaft and the 4 prong from the 1UZ had to be modified and fitted in its place.
The shifter shaft on the 1uz comes out on the opposite side from prado so that was swapped to the other side to match.
Here is the 2 output shafts side by side. Top - Prado (with the 4 prong pickup already installed) / Bottom - 1UZ
Prado case and output shaft with the 2 prong pick up
Left is the 1UZ trans fitted with the prado rear shaft and the shifter shaft swapped
Right the the sad remains of a prado trans
One of the major differences between the Prado trans and the 1uz trans is the rear section of the trans.
This is the prado trans...
You can see the channels are open on the left and right compared to the 1uz trans seen here...
Since the mounting surface of the 1uz trans tail section is quite a bit smaller the side sections have been open to the elements their whole life and need to be cleaned thoroughly before assembly (which I have already done in this picture)
I guess if one got really adventurous you could take the entire trans apart and mill out these sections to match the prado trans but theory has it that there is enough pressure pushing fluid back and forth it shouldn't be a problem. As a side note, I did not opt to drill and tap out the bottom bolt like I've seen on other swaps. I think with the right sealer there should be enough bolts holding everything together.
Another hurdle to over come when converting the 1uz trans to 4wd is the 4wd shifter pivot point.
Prado shifter pivot mount
The 1uz trans lacking of a shifter pivot point
So after a few measurements I came up with a fairly easy solution for this pivot point.
After sorting out the shifter pivot point it was finally time to assemble this whole thing once and for all (knock on wood)