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the P1166 fault can be brought on with a blocked fuel filter and P0401( insufficent EGR flow) can be a sticking EGR valve, or could be down to the blanking plate
As you have already replaced the filter and then also check the connections to the EGR valve and I'd refit the valve to try and clear the codes - you should be able to leave the blanking plate in plate between the valve and the manifold though
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a new EGR needs to be able to move from 1 end of its stroke to the other to 'learn' its position, but this happens every time the ignition is switched on so there's no needs to programme it
I'd say that you may have the wrong type of EGR valve as its sounds like its trying to move the wrong way?