W/r/t "take the area of the port and divide it in two for the intake port area"
Efforts to divide the intake ports vertically (making 6 ports) largely show that the reduced size is more restrictive than the shared port.
Each of the pair of cylinders that draw from a port use it in rotation, not simultaneously. However, the time intervals are not common to the three ports due to the firing order.
The 1 & 2 ports are on intake stroke separated by 240-480-240° of crankshaft rotation, the 3 & 4 have 360-360° separation, and the 5 & 6 480-240-480°.
Unless the program has specific input for siamese ports the results will not be useful.
Have you read Santucci's book?
