In John Baechtel's Engine Math book he states the same formula PortVelocityfps=(Ps/60)*(B^2/Ap)
Where:
Ps = piston speed in feet per minute
B = bore diameter in inches
Ap = area of port in square inches
Same as you had, but then he goes on to say in a picture: To calculate port velocity, measure the port entry and exit and average the two area measurements to obtain Ap. Then plug in the mean piston speed and bore size to find the mean port velocity.
What I suggest is to use Larry Meaux's formula out of PipeMax to figure average port CSA for this formula. That formula is Average_CSA = Port_Volume_CC / (Port_Centerline_Length*16.387)
PipeMax also shows a formula for FPS = (Flow_CFM * 2.4) / Average_CSA
Now if you really wanted to get tricky you would calculate the piston speed for every degree of crank rotation. It does change as per the piston position in the cylinder and whether it is coming up going down and the rod length.

I have been working on this a little myself but have not had much time. I will stay in touch with you if I can find out anything else.