Curtis:
I build Jr. Drag engines and I have had similar experience with the ports and intake manifold. I made my intakes out of aluminum stock on my lathe. I would taper bore the intake at about 1.5 degrees over a 5" length.
I only used round ports with the intakes for the ease of doing the ports. For example: I used a Mikuni carb with a 1.600" throttle bore with the valve seat having a I.D. of 1.500". I would turn down fender washers to the appropriate O.D. and use them for templates to keep the port shape. The Super Flow manual showed an ideal port shape and I used that as a guide.
I guess now I will have to try this on some old V-8 heads and learn from there.
Thanks for the info.