Like Charles I have not done a auto conversion, but have done a manual (1ggteu). Also like Charles I do not believe that the speed sensor has any effect on the auto. I do have a engine manual for a 1ggzeu and there is no mention in the diagnostic codes that indicates any concern. The translation of these codes are in the Tech Docs section on this site.
From what I can determine the speed sensor has three effects (note the signal is obtained from a sensor actuall connected to the speedo). One, once you exceed 3,000rpm for a given period of time - I think it is 30 seconds - the engine check light will come on and store a diagnostic code to this effect. Second, the computer seems to use the speed to determine if the vehicle is still mobile 'cos when it does not get a speed reading when you take you foot off the throttle it gives the faintest beep, - possibly read idle up - to stop the engine stalling. This is not a real problem and is still hard to detect, but now I have told you will annoy the hell out of you. AND three, speed cut @ 180kph.
I have used a cruise control sender connected to the tailshaft to provide the signal to the computer. This solves all of the problems including the spped cut as the signal is only 25% of that of the factory setup and u would have to be doing 720 kph.