HiCustomerand welcome to JustAnswer,
You can try disconnecting the NEG. terminal of the battery to see if that will reset the ECU's memory. There's no other additional adjustments or resets. If that still does not take care of the rough running problem, then you may have another issue here. To properly diagnose this, you need to find out what is causing the running rough issue. What I would suggest to do here is access a scantool to hookup to the vehicle and read the live data it's providing to the engine's ECU. By doing this, you can see what each engine sensor is doing and the values produced. This will be the most accurate way to find out what the engine is doing. Most independant garages have these scantools and all Toyota dealers have them.
Let me know if you need additional help.
I did just that disconectted the negative, lights are still gone and engine seems to be running better, going out for a test drive.
Alright, let me know what happens.