Have you replaced the intake manifold gasket with the revised, orange colored gasket from Toyota? This needs to be done even if it doesn't resolve your issue. Usually you would get the P0171 error code for that, so it might not be the culprit, but just replace it anyway if you haven't already.
Also, when you cleaned the MAF sensor, did you only clean the bulb/wire and nothing else? If so, you didn't clean the MAF sensor. That's inside the plastic tube that sticks out of it.

Also, when you cleaned the MAF sensor, did you only clean the bulb/wire and nothing else? If so, you didn't clean the MAF sensor. That's inside the plastic tube that sticks out of it.