When that CE light starts to flash, that is a misfire and should set a misfire PO300 codes or an injector code.....
A scan tool attached while the CE light is flashing, would be a great help....it would pin point which cylinders are actually misfiring......since you have replaced the secondary ignition parts(plugs, wires, coils), I am leaning towards either fuel pressure, a vac leak, compression or injector problems.....