What year and make is your Yota and does it idle faster when it is cold and newly started then slow down when warm? If it starts with low idle, it could be your auxiliary air valve if you have an older Yota or your IACV "Idle Air Control Valve" if it's newer. This valve draws air into the intake until the vehicle warms up than closes when its warm. I have an 88 22re and my AAV was not retracting to the open position. It's idle was slow from the start and since it was still cold seemed to miss as well. Had to ride the pedal a bit to open the throttle body and give it some air til it warmed up. My valve is controlled by coolant and an electric heater coil both of which warm the valve and close it after it runs a bit. I have heard that some air valves are controlled by vacuum also but haven't seen one yet.

good luck!