What are the codes? There's no problem with running a 3L ATX so long as you're cooling the transaxle "like a mofo" to prevent complete grenading of the thing under the 3L's power, and you have an ADC chip to let the stock ECU take advantage of the extra displacement while still keeping the code necessary to run the ATX.
The DPFE codes (EGR flow excessive/insufficient) can be caused if the silicone hoses are reversed. If you've replaced the DPFE sensor and the EGR valve and solenoid, there should be no reason you're throwing CELs unless something's not hooked up right or you have a bum/misconnected vacuum line.
The DPFE codes (EGR flow excessive/insufficient) can be caused if the silicone hoses are reversed. If you've replaced the DPFE sensor and the EGR valve and solenoid, there should be no reason you're throwing CELs unless something's not hooked up right or you have a bum/misconnected vacuum line.