The "Adaptive Max Limit" fault code is usually as a result of low fuel pressure, particularly as it is both front and rear cylinders, the fuel pressure is a common thing for both. You say you have replaced the fuel pump recently, what type of pump did you replace it with? If it was another standard one it could easily be on the way out from new. I would recommend a Walbro GSS 342, there are full instructions and part numbers on the MTWC website, free access. I would check the pressure at the injector test point, it should be 58 psi. The standard locked ECU should manage to adjust for drilled out baffles in the exhaust, although it will put it nearer to the adaptive limits. You could try clearing the adaptive maps and fault codes in the ECU with ProTune 2 and letting it adjust again?
