The second problem you're going to run into is that the M52 manifold has the idle control valve, oil catch and intake air temperature sensor mounted to the bottom of the collector. The M50 manifold doesn't have the cutout to mount these components. Most people buy overpriced kits to resolve this problem, but the kits usually consist of a few hoses and cheap plastic elbows and t-fittings. While it works, it looks rather cheap in my opinion.
M52/S52B32 intake manifold:
M50 manifold(note there's no place to mount the ICV, IAT or oil catch canister):
I'm currently making a cap that fits over the ICV/IAT/oil-catch plenum. The cap will have a hose fitting drilled/tapped into the side of it and that will attach to the larger hose fitting on the M50 manifold. The benefit of doing it this way is that I'll only have one hose running from the plenum to the manifold collector vs. the rat nest of hoses supplied in the kits.
Not finished yet, but here's the part I'm currently fabricating:
The third issue you're going to encounter is the fuel rail. The M52/S52B32 fuel rail will bolt directly onto the M50 manifold. However, the fuel rail cover will either need to be modified to fit over the larger runners or you can purchase an M50 fuel rail cover. The cover is mostly cosmetic, however it does keep dirt/debris from accumulating around the fuel injectors. The problem here is that the M50 fuel rail cover will not line up with the mounting holes on the M52/S52B32 fuel rail. The kits often include cheap flimsy brackets that extend from the M52 fuel rail bolt holes to the holes on the M50 fuel rail cover. Again, in my opinion this is kinda ghetto.
My solution, I installed an M50/S50B30 fuel rail onto the M50 manifold. It fits perfectly because it was designed for this particular manifold in the first place. However, you'll need to find one from a late model 325 or a '95 US M3 because the early models have the fuel pressure regulator mounted on the fuel rail while the later model 325's and most mid-'96 and newer 318ti's have the fuel pressure regulators mounted under the car next to the fuel filter.
And finally, the last thing you'll encounter is the supporting brackets that attach to the engine block are different. The manifold needs to be securely held in place. The bolts that attach the manifold to the cylinder head are not enough to sufficiently hold the manifold in place. So BMW installed lower supports to hold the manifold in position. Again, the kits come with the same flimsy extensions that they use on the fuel rail cover, or you can do what I did and purchase support brackets for the M50. While my installation method may cost more and be more labor intensive, I feel it's a better design than the kits offer because it's how BMW would've designed it(actually it IS how BMW designed it because I'm using M50 parts).
Hope this helps, best of luck to ya. BTW, here's a peek of my M50 manifold which I painted to match my polished engine:
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