1955-60 carburetor intake manifolds will work on 1955-60 heads and vice versa. However ports are smaller on 1955-56 manifolds and heads. Other differences between years are in attachment interfaces for carburetor(s), generator mounting, power steering pump, and external water ports.
I don't know about the FI heads. There is something different about them and I don't know what it is. The '58 FI heads are same casting as carburetor heads but they have an XX stamped on them which I think means something special was done to them in machining. See
http://www.pontiacsafari.com/L1Garag...dex.html#Heads.
The FI manifolds are in two parts, the FI part and the water manifold part. The water manifold connects the water ports on the front of heads to upper radiator hose.
Interface between the manifold/head water ports changed in 1961 but bolt pattern and gas ports remained the same (I think). The water port difference prevents using 1955-60 manifolds on later heads and vice versa. See
http://www.pontiacsafari.com/L1Garag...ntakeManifolds.
I wouldn't even consider using a '58 FI unit on anything other than a '58 restoration. The '58 FI units are rare, I think only around 400 of them were made, making them somewhat valuable for restoring a '58 to "correct" FI. There is probably good reason that so few of them were made and '58 was the last year. Getting parts for a '58 FI unit would likely be a big problem.