Well it could be the Fuel Pressure regulator, were you able to test fuel pressure and regulator?
It wouldn't be the Injector O-Rings if it were you would have fuel leaking at the injectors and a strong smell of gas under hood.
It wouldn't be the Fuel pump relay or shut off relay because if they were bad your vehicle wouldn't run.
The heated O2 relay wouldn't make it run rough.
Check out the link below and go through the proceedures the best you can.
https://www.2carpros.com/first_things/why_does_my_engine_run_rough.htm
Also I will need more info on your vehicle....
Is it a 1500,2500 0r 3500 and also the engine size in Liters 4.7 , 5.2 or 5.9 ...
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Thursday, April 2nd, 2009 AT 8:37 PM