Dave,
The raised ports etc are not the only thing that can affect the fit up. Head gaskets of differing thickness, Decking the Block/Head surfaces, Angle milling etc all contribute to cause misalignment on the 180° crossover design when the 90°V factor is considered [Think of it as a right angle triangle to work out the dimensional change].
The only way to be absolutely sure of a good fit [ 180° design ] is to fabricate them on the car in question, Heat cycle them a couple of times, then send them out to be coated etc. I built a set for a 59 T- Bird [ 430MEL ] a couple of years ago which we were unable to heat cycle[stress relieve] and there was no way we could get them to fit after coating, still got em , hanging on the wall to remind me, never do that again!
Moral of the story, if you are buying ready mades, ensure that the builder is using at least the same head /block combo on his jig/mock-up that you intend to use in your car. Tell him that you have angle mill etc if this is the case, save both of you a lot of grief later.
Jac Mac