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Did the Toyota Dealer connect to the car with there computer and confirm this ?
Or did they just tell you in general these lights were a pointing to an issue with the Skid control ECU?
If they did plugin and diagnose the issue, what were the code numbers they read from the computer?
You installed the skid control ecu yourself? Did you preform any initialization procedures after replacing it?
Would you be able to get the code numbers, they should be on your receipt. However possible it is for the ECU to be at fault I am always reserved about a diagnoses that points to a computer with out first eliminating other possibilities, at first thought with out any code numbers, your explanation lead me to think that it may be the stroke sensor that is mounted to the brake pedal causing this issue.