Hi Ron.
Quite right - there are actually two considerations. First is that a 4 into 1 system tends to have an extract effect at high revs but not at low, whereas a 4 into 2 into 1 can have an extract effect at much lower rpm. Second is that you can indeed overdo manifold pipe size. The objective is to maintain a roughly constant flow rate all the way down the system (ie you need to design the whole system as a single unit - not design the manifold as a stand alone item) without any one element of the system acting as a throttle.
After quite a lot of fiddling we decided that a 4 into 2 into 1 manifold of the required bore sizes could not be fitted as a single unit, it would have to be broken up and assembled in situ. I thought this was too big a compromise, introducing maintenance issues. Therefore we settled on a 4 into 1 manifold. The port legs are sized to comply with the criteria above, the whole system to match the gas generating capability of a 4.6. And yes the engine has a high torque cam to suit an auto. We'll see how it gets on on the 3.5! The logic here being not to change too much at once, so the box will go in and get debugged on the 3.5 before moving on to the 4.6 and dealing with its carburation/injection and ignition issues.
All that sounds terribly well planned. In my experience engineering rarely turns out that way! For that reason it is always best to make use of the best available practical experience, even if contrary to the theory. This system was designed in conjunction with RPi on the basis that most of their product finishes up in front of an auto box, so they have some chance of knowing what they are up to! As I said earlier, it remains to be seen how it all turns out!
I ought to add that the cast iron manifold is generally acknowledged to be a major drag on the 3.5's performance. Even the slightly larger 3500S manifold is still terribly tight, and what on earth were they thinking of taking the offside branch under the sump and generating an unequal Y! Rule of thumb (subject to getting all the above right!) seems to be that a "decent" manifold is worth a minimum of 10 bhp on the P6. That gives the clue that a lot of efficiency gains are there for the asking, and are so large as to be readily able to accomodate all discussion about port size and auto transmissions. Anyway, I had to have a new system to go around the ZF!
Chris