Could something on the intake side be not registering correctly?? If a sensor is reporting incorrectly, the ecu may think there is more air than there really is. Also, and this would be an "in addition to" situation I think, if there is another problem, the ecu may be running in safe mode. In other words, it might be trying to make it safe for the engine to run by suplying more fuel than is needed.
These are just some random ideas though. They might help, they might not.
"If you are going through hell, keep going."