I can only guess at the reasons for the Argentina Ford engineers to convert the intake ports from stacked (Fase I) to being evenly spaced across the length of the head (Fase II).  At the top of my list would be to get the two center exhaust valves away from each other.  That would promote a more even distribution of heat in the cylinder head.  It’s difficult to say if exhaust manifold life would be improved by evenly spacing the exhaust ports but add that to the list.
 
Without a Fase II cylinder head to look at, it’s hard to determine from the pictures if there was a combustion chamber shape and head gasket change that eliminated the decks being part of the combustion chamber.  If the head gasket became round to fit the cylinder bore, then that would be a positive.  I don’t see any advantage with a firing order change but it could also be an underlying reason for the cylinder head change.
 
There could have potentially been some negative advertising about the stacked ports by competing car manufacturers and rather than just replacing the Ford Y with another engine, it was more cost effective to simply redesign the heads.  And it could have been that the Argentine engineers at Ford just wanted something different that they could claim as their own.

Lorena, Texas (South of Waco)

Looks like Windsor intakes and exhausts would bolt straight on.

Ted.  Why were stacked ports abandoned? 

Here are some pics of the Fase I and Fase II cylinder heads.
 

 

 

Lorena, Texas (South of Waco)

Thinking about it since they were cast a head with just different port arrangement keeping the shaft rocker system that makes sense. It wasn’t retrofitting a newer head.

56 Vic, B'Ville 200 MPH Club Member, So Cal.

Oiled through the block just like ours.

Ted, how were the Argentine heads oiling done. I have only seen photos and a friend I met when I ran Bonneville from the San Francisco area had actually known a lot about them. I believe they were called Fase ll and as you said had a different cam and firing order but kept the shaft rocker arm of our traditional Y..

56 Vic, B'Ville 200 MPH Club Member, So Cal.

very interesting. it makes you think that anything may be possible.(if i was silly enough to do it.) cheers.

Just for fun but still food for thought.
 
Cleveland heads can be put on Windsor engines and vice versa with a bit of cooling passage work.  I've seen this done both ways so it's doable.  While eight of the ten head bolts on the Ford Y do align with the SBF engines, the upper end head bolt holes either in the heads or the block would need to be reconfigured to use SBF heads.  Once that’s accomplished, then the valve orientation in the heads would require a different camshaft and firing order.  And then you cranked up the engine and realized that the rockers were not receiving any oil as the SBF engines do their top end oiling using hollow pushrods.
 
While it’s been considered to use Windsor heads on the Ford Y, it sort of defeats the purpose in that you lose the stacked ports on the Y.  It’s those stacked ports that are a distinctive feature of the Ford Y-Block.  One of the advantages of those stacked ports besides allowing a more uniform length of the intake runners versus an engine without stacked ports is that the intake manifold has a plenum floor that is the same depth under both sides of the carburetor.  If you look at most other engines with a true dual plane intake manifold, you will find a plenum floor at two different depths which throws a ‘kink’ into the torque curve.

Lorena, Texas (South of Waco)

Not going to do it, just looking for fun