When I went to use an early shroud on my short stroke 2.8 (3.2L heads, 46 to 40 PMO manifolds), I ran into two interference issues. The first required enlarging the holes where the induction goes through the shroud.
The second involved interference between one of the redundant bosses on the manifold (there so only one casting is needed to make the manifolds for both sides, I imagine). I solved that one by grinding the manifold.
So I can't swear that any mixing and matching of shrouds and other bits may not take a bit of adjusting.