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A flashing CEL is an indication for a critical component failure. In this case, sounds likely to be misfiring.
You mentioned that it runs rough from 1100 and down, how does the car run at higher revs, does it run smoothly then? Need some details on the car - what was its maintenance history, problem just started or did it get progressively worse over time, how many miles are on the car, what mods if any you are running?
Could be anything from a vacuum leak, dead/faulty O2 or MAF sensor, worn plugs, dead/stuck injector(s), VVTi failure, etc.
Cleaning the MAF first is a good idea, but replacing the O2 sensors and fuel pump may have not been necessary. If anything, they add more stuff to diagnose, as sometimes new parts are faulty out of the box.
First thing I would do is to pull the spark plugs and read the ends. See if there are signs of fouling, detonation, if they are in the correct heat range, excessively worn, etc. This engine is pretty picky about certain parts and their conditions - if the plugs are prefect, but the gap is slightly off, driveability can be affected.
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2002 Corolla S, 1.8L 1ZZ-FE VVT-i
2003 Matrix XRS, 1.8L 2ZZ-GE, VVTL-i (RIP)
2009 Matrix XRS, 2.4L 2AZ-FE VVT-i
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