[NoDOHC]

The trouble with the late intake close P-port is that you might as well go with a side port. All the advantage of the P-port is lost if the intake port closes after pushing 40% of the engine displacement back out the port.

I think that the progressive throttle is the answer, keep the P-port throttle plates as close to the housing as you can get them and run the primary ports normally. The primary ports will not be open after the P-port has closed, so there is no loss of charge air. If you leave the secondary ports functional, your intake charge that just came in the P-ports will leak out the secondary side ports as the compression stroke begins, negating a large part of the P-port benefit (which would be a full compression stroke allowing better torque output).

Overlap is useless under vacuum, but does not hurt that much at WOT. In fact, with a well tuned exhaust and intake, the engine will actually flow unused air from intake to exhaust during the overlap, slightly cooling the combustion chamber and increasing net thermodynamic work from the next air/fuel charge. This will increase Volumetric efficiency and torque output.

If the primary ports (with no overlap) are used for idling and cruising, and the peripheral ports kick in only when the gas is floored, the car should have good driveability. I was going to use 6-460cc/min injectors, 2 in each p-port and 1 per primary port (in the center iron). This should give a decent transition, especially if the engine was tuned on TPS.