CNC porting has been around quite a while and adds consistency to port work. Hand port work is done line of sight with a only few measurments that can be taken. Invariably some ports turnout a little better than others. The Y-Block lower port is so particular to the shape, height and drop off of the floor to the valve seat that consistency is difficult.
Why not incorporate these changes into the castings? Ted is 100% correct. We need to be able to sell the heads to any Y-Block owner, even if they only want them as replacement heads for a stock 55 T-Bird 292. One size fits all just won't work. The ports in the standard heads are small enough to work on a stock engine and are still capable of 400+HP on a well built engine. CNC porting is for the people who are going to race or just want more than everybody else.
Theoretically, we could make a second set of core boxes incorporating the modified ports but then we would have standard head castings and race head castings. This would cost 1000's of dollars and there would be a limited-run premium on the race heads anyway. Plus, how many of each to order? Worse yet, what if the the foundry gets confused and casts heads with race exhaust and standard intake ports? Race upper, standard lower port?
With regard to various levels of porting it isn't as easy as you might expect. A head must be ported to that level, upper, lower, exhaust and chamber. The information must be captured with a digitizing probe. The program must be massaged to remove excess information and to join the information from the intake gasket side and the valve seat end of the port. No probe can can get the entire port from one end. So, other than the fixture work and some basic dimensions, its kind of like starting over.
http://ford-y-block.com 20 miles east of San Diego, 20 miles north of Mexico