SoupNazi

In August my wife was driving home and the car started to slow down and she couldn't accelerate past 20 mph even with the pedal to the floor. At stop signs it would shake pretty badly and the cel and AT lights came on. She got home and parked it and I took it to get the codes read. Of course the AT was acting fine but the cel code was p0606. I disconnected the battery to reset the codes and cleaned the throttle body because it had been a while and found that the wiring to the egr valve was disconnected. After the cleaning and resetting it was fine until this weekend. This time I was driving and the car coasted to 20 when we were going home. The next day the AT light was off and the cel was on again and read p0606 so I ran some errands and the fourth time I started the car since the episode the cel went away on its own. In august the weather was a normal sunny day and this past weekend it was 0 degrees Fahrenheit. Could the shaking have caused the p0606 code both times and is the ecu screwed? What would cause the AT to act in that way assuming the ecu isn't the issue?

I have a 2006 3 2.3 5spd auto with 130k. The car hadn't had a tranny flush by 100k so I haven't done one.