I need to drive one that is a 5 speed, I suppose. I don't see how you could run it on the stock ECU though, because the engine would face loads that I would imagine are off the map on an ECU set up for an automatic, it seems that i remember that people were having stalling issues... I am also concerned about the clutch setup, etc... all of which have to be rigged. I suppose it would be easier than the new 4eat, but I don't know. Hopefully the new OBD II 4eat would run off the TCU without engine input, if it will, then the wiring would be as easy as adding the harness from the donor car, but i doubt it is that easy.
The real answer would be to figure out how to mod the car to accept a toyota/aisin transmisson.