Have done this many years ago and I used the gaskets as a guide to match the ports to the manifolds and used burrs to do the areas that needed the most metal removed and various flap wheels to smooth out any casting roughness in all 3 components for the best result.
Take your time and don't rush.
IMPORTANT you must not POLISH past the where injectors enter the inlet manifold but can use flap wheels past them for a slightly rougher finish much like cylinder bore honing finish to help better air and fuel mixing.