AEM Really does a great job at making the initial startup easy for the end user.
When you first connect to the AEM V2 you simply go to "file" then to "open" then "calibration" from here go into the AEM folder and select AEM Tuner and then toyota. There are three base calibrations to choose from. Select the one that best fits your setup.
With that calibration loaded into your ems the next step is to setup the sensors that you have.
Go to the wizards function on the top of tuner, and select "setup wizard"
The main areas of focus are.
Air Temperature
Cam/Crank sensor
Coil Dwell
Coolant temp
Map sensor
O2 sensor
Primary inj batt offset
The goal is to select all the hardware that you have and the wizards automatically setup each sensors calibration.
The next step I take is to wizards once again and then to change injectors/pressure input 550cc for the old selection and then plug in XXX for the new selection.
Doing these simple steps will get the vehicle to the point of driving it to where you will be able to bring it to a tuner, and they can tune the afrs and timing accordingly.
And will save you $$$ over taking a class or having a tuner do the base calibration.