Are you very sure that the EGR was totally blanked? Dark smoke would sugget a lack of burnable airflow.
Have you, or anyone else, done a compression test?
Could any part of the intake path have internal damage, a foreign body, or be delaminating?
Can't find any useful data on that engine; but random thoughts:-
Has it got variable valve timing?
Has the cam-belt jumped a notch?
Has it got intake manifold runners?
Could it have a broken valvespring?
What fuel is in the tank?