M54b25 engine rebuild, common issues??

Hey Guys, I'm planning on getting a e46 wagon from a coworker of mine, he was in the middle of rebuilding the engine and converting it into a manual. He's an older tech at my job, but he also has his side business so he got too busy for the car. Since the engine is already out of the car, I want to go ahead and deal with any future issues before I finish rebuilding the engine and throw in the wagon. I heard the m54s have a big overheating issue, and the oil pump gear backing off, do you guys have any other stuff yall would recommend doing while the engine is out.