Theres two integral parts to an engines operation that critical in making it run right. You cant have one without the others, and you need both working in sync or you'll get a rough, or worse, no idle as she wont go. Fuel and spark are those two things.
It sounds like you've covered most of one side, short of a coil or some other electical problem, I think you have a problem on the fuel side. I would be starting with checking fuel pressure. I would also check that the injectors aren't clogged up. If you find that the fuel is stail, it's most likely the whole system will need a flush including replacing a fuel filter.
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