For Mopar intake porting the other guys here should share their experience.

I can share what I know from comp heads and pro stock stuff.

In many cases it's good to have the intake opening very slightly smaller then the head opening. The small lip left helps tune the shock wave that travels the port.
On a head that may have too large a port for the engine combo, .. leaving the port opening small can also have a very good effect on port velocity. We used to run oval port intake manifolds on square port bog block Chevy heads and pick up .3 - .4 et all the time.

As for the rest of the manifold, .. porting & tuning on an all out head / intake combo is critical. The head & manifold together form ONE intake runner right? So the intake runner cross section & volume is just as important as the runner in the head.

On many combo's the gasket area, where the intake meets the head, becomes the smallest area of the entire intake runner.
A properly designed intake runner should not have the same size ( area & cross section ) all the way down. Just a strait pipe from the plenum to the valve wouldn't make power.
There has to be a little venturi in the port where it get's a little smaller to effect air speed. How far up or down the port this is located depends on the combo.

If you really want to know the entire airflow story in an engine, ..
flow the exhaust port with the header that it's going to run with, .. and the intake & carb on the intake side.

When you get this far into a project, .. it's a VERY good idea to turn the head around on the bench, push the air out of the bench into the intake, .. so you can do a velocity map of the airspeed coming out of the valve.
This is a good time to do wet flow since the set up on the bench is the same.

Curtis