Hey Bryce,
Did you resolve the problem? Was it the ECM in the end?
I recently bought a 2002 RAV4 and am expereincing similar problems, although I am getting the Check Engine Light coming on after driving for 2-5 min, O2 sensor error.
I have replaced all 4 O2 and the MAF Sensors, however it still persists.
I was considering replacing the Catalytic Converter, however, I have decided to do the ECM first and see if it resolves the problem. Picking up a refurbished ECM tomorrow.