I would love a manual swap in my 4Runner. It would take care of my biggest complaints with the vehicle.
I did an Auto to Manual swap in my 90 Nissan 240sx, and it was easy enough. It even had the clutch pedal bracket already welded on the firewall from the factory. It was pretty much just a bolt in affair, and I kept the Auto ECU, and just tricked it to thinking it was in park all the time, so it would start...
I don't think today's electronics would make it very easy for us to do the swap though. I would assume you would need an ECU from a 1GR-FE w/ a MT, and from there, who knows how it would interface with the rest of the vehicle.
I guess since LC Prados do have the option of a 1GR-FE with a MT, it would be possible to get the parts you need by importing a Front Clip, or Half Cut from Japan in the future, I just wounder how you could get it to work.