Fuel pump or pressure sensor is my bet, sometimes there will be a ticking/clunking sound when you turn the car off after it has been running rough (turning car on and off again stops the noise), this is normally a good indicator its the fuel pump, you can also turn on the ignition (engine off) and see if you hear the fuel pump start cycling after a while. It's also a pain to change the fuel pump as you have to of course drop the fuel tank to change it out, make sure you grab a new gasket when you order the new pump.
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