The air pump & EGR are not the same thing.
First, the EGR (Exhaust Gas Recirculation) sends exhaust gasses from your exhaust manifold back into your intake manifold in an effort to reduce emissions.
The air pump is also there to reduce emission. If I understand correctly, it force feeds air to your engine for a while after a cold start to reduce emissions. Someone correct me if Iím wrong.
I canít speak for your car, but I did disconnect the EGR on my 95 GTi VR6 and my 97 Jetta TDi when I had them with no ill effects. I also installed a supercharger on the GTi and in the course of installation; the air pump had to be disconnected. The car ran really rich with a cold engine after that, I couldnít say if it was because of the air pump being removed or the questionable engine management that came with the supercharger.
Why are you getting new manifolds?
You have a euro model, did you get headers?
I'd love to get some good *affordable* headers for my 420SEL.