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If you have changed all spark plugs and coils and have spark on all cylinders but still have a cylinder misfire or rough running this fault here can be caused by a fuel injector that isnt atomizing properly.I have run across this issue several times before and had to in some cases clean the fuel injectors to correct this here or replace the affected fuel injector.
If you have not had the fuel injectors tested this needs done to see if one or more are at fault.This usually requires a scan tool to pulse the injectors one at a time or an injector pulse tool and a fuel pressure test gauge to monitor the pressure drop.The fuel pressure test gauge is installed and the fuel pump primed then one injector pulses.Observe the fuel pressure before the pulse and after and subtract the two to get the fuel pressure drop.Then re prime the fuel pump and pulse the next injector and calculate and record the drop pressure.They should all drop evenly.If one is found to drop 1.5 psi more or less then the rest of them this is an issue and the injector needs cleaned or replaced.In some cases just adding injector cleaner to the fuel tank will help clean the injectors and I recommend doing this at 1/4 tank with a bottle of cleaner and run tank to near empty and repeat.In other cases the injectors need cleaned with an injector cleaning machine to correct this here.When the injector affected does not clean to correct this fault then it will need replaced.
If the injectors test o.k. and you do have spark on all cylinders this can be a fault with low cylinder compression on one or more cylinders and most common is a burned or damaged cylinder head intake or exhaust valve needing replaced.I would have a cylinder compression test done to see if one or more cylinders are found low on compression.The compression should be fairly even on each cylinder with each other and any cylinder that is 15 psi or more different then the rest indicates a fault with cylinder compression needing resolved.
The other issue I have seen is a dirty or faulty mass air flow sensor.I have seen the mass air flow sensor send incorrect air flow signals to the engine computer causing issues like this as well with the mass air flow sensor needing removed and cleaned or removed and replaced for this issue here.
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