Check that air is able to get in to your tank. If you are pulling a vaccum as the fuel is pumped out it will cause fuel starvation, which could give a problem like you are describing. Fast way to check is to undo the fuel cap when the car is playing up. You will hear air being sucked in to the tank and the running will return to normal if this is your problem.
Best of luck with fixing it.
Enoch
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