Stump, interesting post, but I hope you don't mind if I play Devils Advocate!
First, I have nothing but distain for JMS, his shoddy procedures and how he cheated folks, but I also remember some of the 064/660 saws he sent to the CT GTG and I will tell you they were VG runners, so he knew something. Perhaps they were just his "I got lucky" saws that he saved to send to us, I don't know, but they ran.
Secondly, I have had this intake debate with other builders, and my thoughts are that is it similar to why the lowers are larger than the uppers, which don't even fully open.
1) The intake goes into the crankcase, not directly into the combustion chamber, so IMO volume is more important than velocity. If the upward piston movement generates 5 psi of vacuum, the more area that exists when it first opens the more air/fuel mix will be sucked in.
2) For the upper transfers, direction and velocity are important, and if the lowers have more area for the pressure, this will increase the velocity of the uppers. It is like a garden hose, the larger the diameter of the hose, and the smaller the spray jet, the more velocity you will have.
Those are my thoughts on these issues, for whatever they are/or are not worth! Opposing comments are always welcome!