2006 E350 Engine Swap Questions
 

I bought a 2006 W211 with multiple misfires on cylinders 4,5, and 6 thinking it was likely an issue with the catalytic converter. I unbolted the driver's side exhaust and ran the engine, no change in idle. I took it to an independent MB specialist who did a (half-a**) diagnostic and told me it needs the engine replaced (quoted $6,400). I'm currently sourcing a used engine to install myself, a 2009 E350 engine. What parts will I need to retain from the 2006? I know I'll need to keep the ECU, do I need to do anything to pair the ECU with the 'new' engine? Is there anything else I should look out for? Any parts I should replace since I'll have the engine out?

I hope you've got 2nd opinion?
Right now even $150 scanners run smoothest aka compression test on those engines, so not big deal to troubleshoot DIY.
If you go for engine replacement, all original modules have to go on new short block. At least on diesels injectors are also programmed. Otherwise you are facing system reprogramming what can turn into nightmare.
You did not say what's the mileage? MB cylinders don't just give up for no reason, so investigating what happen might give directions to future actions.

Thank you for your replay! It's a gasoline RWD model, 126,000 miles. It starts and runs, but very rough, stalls immediately when put into drive or reverse. I would certainly like to get to the source of the problem, but I can get the 2009 motor for $1,500, so I don't want to spend a lot of time/money diagnosing an engine that may end up needing to be replaced. What modules will I need to retain besides the ECU? I'm not too familiar with the other modules - I've done rebuilds on Subarus, but this is my first MB experience.

126k miles is not much for those engines, so chances are that your short block is good and you have electronic problems.
Would suck to replace the short block only to find that it did not cure the problem, wouldn't it?
I am not familiar with gasoline engines, but you should find diagrams on google, or maybe member knowing your engine will come forward.
And again, would not hurt to mark old injectors and have them waiting just in case.

Well the 2006 was well known to have balance shaft problems. You should get a scanner that reads MB codes though to get a more complete diagnoses. What are the codes you're getting now? Misfires are typically plugs and ignition coils, but sometimes they can be more complex like fuel injectors/pump etc. There's lots of little things that can go wrong on the engine, oil separator, oil cooler gaskets, camshaft/crankshaft sensors, thermostat, pulley/tensioner, intake manifold etc. You're better off with a low mileage engine.