Rough running 2001 Prius

My Prius is having the same issue. Did you ever get yours fixed?

I have not been able to find a solution yet. My local Toyota dealer cleaned the throttle body and says this cleaned the Idle Air Control Valve(IACV). I then decided to replace the IACV so the next nearst dealer told me $1200 to replace it. This sounds like replacing the whole throttle body. The 3rd nearest dealer to me said there is no IACV, but a wire controlled by the computer.
I'm still getting 46+mpg suburban driving so overall so the rough running is not affecting my milage, and the Check Eng light went off for 1 day last week so I took it in and passed the "smog" test. Maybe a small piece of electrician's tape will fix the light, but I still do not know what to do about the rough running.
Let me know if you find a fix, I seem to have hit a wall that I can't get over without a lot of cash.

Just to help narrow it down, which of these things listed above can make it run rough only after the gas engine was off 3 minutes(hot or cold) or more, but still runs great after less than a minute and still gives me fantastic gas mileage?
I'm not a mechanic, but it seems to me that all these listed possibilities would hurt the gas mileage or would result in a constantly rough running engine, not temporarily and only after 3 minutes of down time. If off for anything less the gas engine runs fine.
It almost sounds like a programmimg issue to me. I really appreciate your time on this.