When I did this on my Europa Special I just matched the head ports & cast iron manifold to the gaskets, so you also need to check the gaskets are also not impeding the exhaust flow.
Never port to gaskets. Gaskets often are oversized to allow room for improper alignment and movement for those who just sparingly place them on . There made just to seal. They do no flow research.. Always port match. This is exactly what this gentlemen is doing correctly.
Sorry mate, if the exhaust header set has been correctly built on a proper jig, the port matching work you are doing would not be required. We have built three header sets for our twinks, the exhaust manifold flanges are either laser cut or machined on a lathe (Bores and faces) and then jig drilled for correct head port match. But if they are a real mismatch then what you are doing is correct.
