My Brother-in-Laws 2000 E39 car got stolen and they cooked the engine. He purchased another M52 engine and there are things different on it, He was told it came from a 1999 E39.
The exhaust manifolds have a different shape to them. The old engine had the manifolds coming out mid way and pointing to the rear.
The new engine has the exhaust manifolds coming out more to the rear and pointing down.
He tried changing out the intake manifolds and they are different also. The 2000 M52 has elongated "D" shaped ports and the new engine has elongated "Oval" ports.

Both engines are marked on a paper sticker by the flywheel as being M52. I am going to try and post a picture of the paper tags by the flywheel. If anyone can help I certainly would appreciate it.
Also, there seems to be something different about the Vanos. I could not get to it to see today really good but the 2000 engine has something kind-of like a cylinder tensioner on the front of the engine whereas the new engine he purchased does not appear to have it. Both engines are aluminum head.