Matching the manifold to the port will help flow in theory but it may also increase any tendancy for exhaust gas reversion to occur. If you tend to get reversion (does the inside of your carb get black?) then making the manifold slightly bigger than the port will reduce that and keep the intake mixture cleaner.
Flow into the manifold can be improved by sloting the stud holes and raising it slightly until the floor of the manifold lines up with the floor of the port. This puts the faster flowing gas at the top of the port closer to the center of the manifold opening. But if you do get a lot of reversion then you are better off leaving a step down at the bottom as this is where the slowest gas speeds are and it is the slower gases that tend to get drawn back into the cylinder and intake.
Another trick you could try is using a spacer between the head and manifold (using an extra gasket and longer studs or bolts). This moves the restrictive angle into the manifold farther away from the port. But to be effective you need at least a 1/2 inch thickness. The extra flange may be slightly larger than the port opening in the head, but must not step down entering the manifold. Do not taper, blend, or bevel the extra flange to act as a transition between the port and the flange.
