Did it start running badly all of a sudden in the past few months? Or has it been a gradual process?
If the thermostat is stuck open, or the engine is one the verge of overheating, that could also be the issue.
Does the engine start quickly and run good when cold? It almost sounds as if the engine control unit is keeping the mix rich (as if the engine is cold) even when the engine gets hot and should be running on a leaner mix. Did they unplug your ECU and plug in a replacement? If the coolant temp sensor is working OK, and the wiring is OK and the fuel pressure regulator and injectors are OK, then I would think that swapping in a known good ECU would be the next thing to test.