I did the exact opposite of you, swapped a 5-speed into my '99 4runner.
I will tell you right now going from Auto to Manual is easy, going from Manual to Auto will be tough.
The manual transmission you have in your T100 is an R150F, the R151 only came on the 22RE Turbos. The A340F will bolt up no problem. The transfer cases don't need to be swapped, all 5VZ transfer cases are swappable.
The R150F is ~1.25" shorter than the A340F (depending on the year). If there is enough travel in your slip joint in your driveshaft you won't need to find another driveshaft.
Yes you absolutely need the computer from an Auto. This will be the hard part, finding the correct computer and wiring the Auto transmission properly. There are 4 or 5 electrical connectors that need to be hooked up. The easiest thing to do is to find a wiring harness and swap harnesses with your truck. Then you need to swap your radiator to run the transmission fluid cooler lines (or make a transmission fluid cooler of your own). You'll need to plug the hole where the clutch goes through the firewall, and you'll need to plug the hole in the center console (and I want to say the Autos in the T100s were column shift so you need all those parts, but I could be wrong). It'd be a lot of work.
Out of curiosity, why would you want to switch from Manual to Auto? Most guys (including myself) prefer a manual (hens why I did the swap). If you want an Auto T100 have you considered buying one and selling yours?