1993 Chysler Le Baron is missing badly and smells of fuel

I have a 1993 Chrysler Le Baron convertable 3.0 v6 automatic(4speed) with 126k miles. I have just had the transmission rebuilt and all was running smooth, so I thought. At this time the check engine light has come on and while the car is running it smells of fuel badly. When the car is idling or driving it feels like it is missing and causing the car to run very rough. Any ideas on what would cause the missing as well as the fuel smell? I checked under the car and found no fuel leaks.