Engine Control Module Code and Rough Idle

[rks171]

My 2007 Yaris has had a rough idle that comes and goes for over a year now. My attempts to fix it have included changing the spark plugs, cleaning the mass air flow sensor, and changing the air filter. I have changed the battery a year ago when the old one died. The car has about 140 k on it now. Within the last month, I've now been seeing the check engine light go on and off periodically. I had the car scanned and the error code is P0606, which says it's something related to the engine control module (ECM).

The guy at O'Reilly says it doesn't necessarily mean the ECM itself is faulty. He actually believes it isn't the ECM itself because the check engine light doesn't stay on all the time. He thinks it's something mechanical. From what I read, this error code can be a real pain to diagnose, as it can be caused by a lot of things from corroded wires, to faulty connected sensors, to the ECM itself. However, I'm wondering if that rough idle might give indication as to what is triggering the error code. What else could cause the rough idle that could also cause the ECM to complain? O2 sensors, MAF sensor?

My last resort is to take it to the dealer and have them try and diagnose it, but I hear that can get expensive fast. If they hook it up to their computer, is it going to tell them exactly what is at fault in the system?