It sounds like you have ruled out most mechanical issues with the engine, so I would be looking to electrical components. Check the condition of your plugs, leads, cap & rotor button (if using a distributor) If not, check the condition of your coil packs.
If your plugs arent fouled or bridged with deposits, then it could be an injector not spraying as well as it should. But generally if you have a problem with a particular cylinder it will show up on that plug.
Failing that, if you have an aftermarket ECU you might be able to check its log to see if it recorded anything out of the ordinary.
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