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Hi Doug,
I have a similar problem - see my posts under "jkordzi" You can see all the things I've done to try to isolate it. Although I have yet to isolate the problem, I think I've eliminated a few things. FWIW, here's my advice. Since you have reported that the cold boot improved the situation, it would seem to me that the problem is in either the ECU or one of the sensors that the ECU uses. Most of the time, the ECU will pick up a bad sensor and set a code. However, from my experience with other computer controlled cars, I do know that this doesn't always occur. These sensors are typically monitored by the ECU by sending out a known voltage (e.g., 5 volts) and then monitoring the voltage received back from the sensor. Because each sensor has a specific internal resistance, the voltage received back by the ECU is less. The ECU knows the range of acceptable voltages. If the received voltage is out of range, a code is set. This covers most failures which result from an open circuit or a high resistance, but may not cover a sensor that is going bad, has yet to be out of range, and is simply reporting the wrong value. For instance, a failing O2 sensor may not set a code, even though it's on its way out and is dragging down your mileage. This type of problem may be what you have. The only way I know to find this kind of problem is by successively swapping on known good sensors. Alternatively, it could be a bad ECU. Lastly, I think it's possible that you have a bad ground or bare wire somewhere that is intermittantly causing a sensor to send back a low voltage, causing the ECU to adapt to it and incorrectly adjusting the fuel/timing/etc., which is reset when the battery is disconnected.
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