sptt, what brand and rating is the thermostat? Is the water pump aftermarket or genuine MB?

The shop that did the engine swap should have ensured that the engine/cooling system was performing properly before considering the job complete and allowing you to drive off. You need to find a reputable shop that knows MB automobiles and how to work on them. No responsible shop would return your car to you with those issues, knowing the recent history.

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Fred Hoelzle