Do you have the capability to scan and log data? If so, see if you can log your misfires, then try swapping the ignition modules on the air breather and see if the misfire moves from one side to the other. Also, pull your plugs and check their condition. You could check the rubber plug boot between the coil and plug while your at it. Look for tracks where it might be arcing. Also check the accordion boot between maf sensor and y-pipe, if it's split, you'll get false air and incorrect fuel metering. I've seen this personally on many occasions on all types of cars.
These are probably the most probable causes for rough engine performance.
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