Not sure if this is the case but if you've blanked off the egr valve but not had it disabled then i think the ecu will react to the feedback voltage of an operating egr valve that may still stick open.

I've just had a similar problem with a Z16SE auto astra where the egr valve was faulty, i fitted a blanking gasket (1 port hole) and for some unknown reason it still caused running problems when the egr valve stuck open.

This can only be caused by the ecu altering timing/fuelling in response to feedback from egr position.

I'm happy to be corrected but this was fact with the Astra i had problems with as a new egr valve and gasket (2 port hole) has cured the fault.