Not in any particular order:
Check your ECM to see if there are any diagnostic codes
Check coolant level
Are your plugs wet with fuel?
Check cold-start injector time switch - may not turn off injector
Check to see if your brakes are dragging.
Check for vacuum leaks in your intake system or pcv system.
Check egr valve to see if it is staying open
Check your air filter
Are your ignition components DENSO or NGK brand? Many ignition components are substandard for use in Toyotas.
Check your ignition timing
Check your cylinder compression
Check the following sensors:
Air flow meter
Coolant temperature sensor
Inlet air temperature sensor
Throttle position sensor
Download service manual: