I'd start by looking at the air intake. Check to see of there's a build up of thick carbon deposits inside the inlet manifold, and that the EGR valve is not stuck partially open. Check to see if it's clean and can move freely from fully open to fully closed. If the inlet manifold is clogged up then the best way to resolve it is to remove it, and after first removing the worst soak it overnight in a bucket of a 50/50 mix of water and traffic film remover. A filthy job, but your engine will run a lot smoother with a clean air intake.