Just came across the thread. A little confused. You said there was oil in the crankcase, but was there coolant in the radiator? Coolant being a little low is not a big problem, empty or nearly is. If there was no coolant, then it is a certainty the engine overheated and scored the pistons and cylinders, possibly cracking the cylinder head. It would would be hard to start, could smoke, and could run poorly. This would necessitate an overhaul.

As others have said, best to do a compression test on all cylinders first. Harbor Freight sells a relatively low cost tester, good enough for occasional use. All cylinders should be about the same.

Another thought: maybe it dropped a prechamber tip. The end of a prechamber can crack and break off, falling on top of the piston. This could have been the "thud" you heard. It will cause the engine to run poorly, miss, and emit black smoke since the fuel is not being atomized properly in that cylinder. You can check for this by removing the injectors and sticking a piece of wire into the prechamber hole. if one goes further than the rest, the tip is broke off. Be aware there is a ball in the center that may stop your wire prematurely (if it has not burned up) and you need to work the wire around it. If this is the case, it is not a great situation but may be salvageable by removing the head and broken part, and replacing the prechamber. Can beat the piston up pretty bad.

As for a replacement engine, the W110 200D engine is a slightly better engine as it has 5 main bearing rather than 3. Otherwise it looks pretty much the same from the outside and most parts are identical and interchangeable.