The engine ecu is also the transmission control ecu. You will need the harness and ecu for the model/year vehicle. Some of the body harnesses have different plugs when switching from manual to automatic. This could create the need for a custom harness/cut and splice. If you have a wiring diagram for your model year, look at the engine ecu and see if there is a difference in connector name from auto to manual.
I can rebuild a manual faster then an automatic. I don't think either one is easier though. The auto will require less press work but more difficult clearance measurements. If you can do one, you should be able to do the other. A quality automatic build requires a cleaner person/workspace. A manual can live through a dirty technician but not an auto. So many seals, o-rings and small passages can't handle any dirt
I didn't like having an auto behind my 3.4 supercharged. It felt way slower/weak. The torque converter loss just seems to be too much. Overdrive is way too tall. When running loaded, I could slip the converter before it would come out of lockup. I was able to up the line pressure and change brands of fluid to stop that.
I'm not a 100% sure what IPT does, but shift points will still remain the same as they are ECU controlled. I'm sure they just raise the line pressure and change the accumulator springs to make it shift more firm. Remove some designed restrictions in the valve body plate so the clutches apply faster/firmer. Will it make up for the drag of an automatic, I don't know. I'd like to try/drive one though.
2004 4runner just starting to build
83 Hilux SR5 is being sold
94 pickup in a pile of parts