If you look at the actual FJ tcase in his first pic, which I assume is the one that he actually has, the input shaft of the tcase is the same as the stock 4R tcase.

The FJ tcase in the second pic appears to be from a manual shift, 6 speed FJ from the input shaft or is just missing the female collar on it.

Note that the FJ tcase from the manual 6 speed FJs won't work on the A750 auto trans in the 4Runners. You MUST use teh tcase from an auto.

Also note the some of the 5th gen 4Runners have manual tcases that are identical to the FJ tcase. These can also be used for this swap.

And option to retaining the front diff ADD system is to eliminate it and replace with the same, solid axle version that the V8 4Runners use. See the following link. Same parts/steps for a 4Runner as the Tacoma.

How to: Deleting ADD system | Tacoma World

@ryanking61 , great choice on doing the swap! Following along and willing to help with any questions you might have along the way. I know mine's a V8 but the swaps are virtually identical otherwise. Lots of swap info on the tacomworld 2nd gen forums as well.