If you're going to take the old engine out, then it might save you a lot of time to clean up the new engine and fit new parts onto that one instead of repairing the original engine.
The new engine probably only needs a new cam-belt and water pump to be ready to fit, and that will be easy to do while it's out of the car.
I wouldn't worry about cleaning it out inside, before fitting it.. once it's installed, just put some cheap oil in it (0W30) plus some engine flushing agent .. or use flushing oil... start the engine and let it fast idle for 20 minutes, leave it overnight, do the same thing again and then drain the oil. You'll be amazed what comes out of the diesel sump..
Let it all drip out, then replace the oil filter and re-fill with clean oil. It'll be cool.
When the old engine is out, compare the other parts like the alternator, if the new engine has everything attached. Swap over the part that looks in best condition. Alternator is tricky to replace in the car because one of the bolts is very inaccessible when the exhaust and driveshaft are fitted... so check it while the engine is out.
Also check the clutch (100,000 miles/160,000kms seems to be the release bearing life, even though the clutch plates last longer) and the Dual-Mass flywheel (180,000 miles/290,000kms)..... and look at the driveshaft oil seals, since these are difficult to fit on the car and just cost a few Euro's .. so change them if they look like they're leaking. Buy 4 because they can deform easily on fitting...
The airbox is a work of art... but a complete PITA to seal properly. The rubber neoprene connector on top of the metal pipe under the turbo can get loose and leak, which will make you smoke... so while you have all the pipes off, just de-grease all the internals, check the condition and fit some new clamps.
100,000 miles/160,000kms seems to be the life of the Turbo boost actuator valve. It lives under the headlamp with the airbox in front of it... so if yours is likely to die soon, change it now.. and check all the vacuum tube is good and not leaking. When the valve stops sucking you get poor boost and the engine smokes a lot. My Turbo boost actuator is still the original but check yours moves easily when the valve sucks on the pipe. They're not too expensive and it's easy to replace it with the engine out.
While the engine is out, also remove the pipe to the EGR valve (under the thermostat)... it will be full of carbon for sure... so give it a good clean. The EGR can also use a clean. I blanked mine off to keep it clean. The car makes more NOx pollution but goes slightly better and uses less diesel (less CO2, so me and the planet are cool.. ) EGR is okay to change when it's in the car... but the pipe is going to have rusty bolts... so best tackled off the car.
Oh... don't look inside the inlet manifold....

butif it was me and the engine is all in bits, I'd take it off and clean it out. It looks like oily syrup in there and it can eventually pollute the EGR and the MAP sensor (the black plastic tab thing on top of the manifold).
If you're in Finland, you'll have long days soon... but in case you don't make it, sir.... good luck!
Ralf S.