Enging runs rough and when in gear barely moves if at all?

Hello, The flashing check engine light is a warning to shut the vehicle off. If the transmission will not move forward, back, or quickly, it likely will need to be rebuilt or replaced. Let me know if you have other questions, otherwise, here is a list of certified shops for your convenience. http://repairpal.com/toyota-within-10-miles-of-el-dorado-hills-california-95762