There is supposed to be no Vacuum in your Intake Manifold.

Some of the Older Mercedes Diesels without a Turbo have Fuel Injection Pumps with Pneumatic Governors have a Butterfly Valve in the Intake Manifold to create Vacuum for the Governor.
Otherwise Diesel Engines do not create Vacuum in the Intake Manifold unless something is restricting the incoming air (plugged Air Filter or as stated that Butter Fly Valve).

When was the last time the Air Filter was changed?
If you have a CA car for sure you have an EGR. The EGR could be opening a little at the wrong time or sticking.
On mine the EGR is controled by those White Plastic 2/3 Way Valves (correct name?). May be those valves are sticking and keeping the EGR open when it should not be.
When your car is running good pull the Vacuum hose off of the EGR Valve and plug the hose. Drive the car and see if your symptoms go away.

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84 300D, 82 Volvo 244Gl Diesel