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Without having the code it is hard to say what is going on. Click on the link below for a copy of the bulletin that I believe you are talking about for the transmission. There is probably an insulation fault in the motor windings. This is a serious problem. You need to leave it with the dealer to get it taken care of. I find it hard to believe it takes a month to fix or get the part but it depends on if there has been a rash of these going bad at any one time.
I would see if they have a loaner car or if Toyota will provide a rental car because it is under warranty and the car can't be driven until it is fixed.
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Not know which code or information sub code we are dealing with it is difficult to say with certainty. The car will eventually not start if the insulation short is not repaired. If your dealer is uncertain of their diagnosis find a competent dealer that has a good hybrid guy. Honestly they are few and far between. If you are near Cleveland look me up.
The cruise will shuts itself down on a malfunction light. There is a possibility there could be a wiring problem outside of the transmission but that is doubtful. The hard braking demands more from the regenerative breaking systems in the transmission so that explains the insulation break down more then likely. This is all speculation at this point with out running proper test. This is a very complex system.
If it is a salvage title Toyota will not warranty it. The transmission is about $7,000. I would pick the largest dealership in that area. They will have the most resources available to pay a high end technician. I am not that familiar with anyone in that area.