Something is telling the ECU the engine is doing 8000 rpm and it's dumping 8000 rpm worth of fuel in at ~2000 rpm, therefore it runs rich. Well, that's one possibilty anyway.
Are the cam/crank angle sensors OK (when tested as per the Toyota manual)? Is the sensor calibration correct? Are the sensors receiving the correct voltage? Is there some sort of 'cutoff' or 'trigger' voltage/current that is incorrectly set? Not sure how the Microtech does all of that (I'm not at all familiar with them), but there is clearly some funny business going on with engine speed detection. The fact it comes up with an RPM warning suggests there is an issue OR it might just be that it thinks you are overspeeding the engine.
Do Microtech have a 'support desk' at all? With all the 1J conversions going on, surely this is one they must have done. If they do, there will (hopefully) be a database of common probs.