Good question with an answer that may be hard to swallow for some. I will not port match the heads to the intake or the intake to the heads. It will go on as is with the exception of minor touch ups wherever the casting may be flawed.
A mismatch or step especially where floor meets floor can be beneficial and produce more power. Some say it curbs reversion and some feel the flow disturbance produces "eddy's" that promote mixture motion and better combustion. I don't know what really happens but I do know and have witnessed power losses when port matched. Here I am talking "average power".
Peak may be slightly better but average usually suffers. I am shooting for driveability and that includes part throttle tip-in. No port match here. J.Rob
Forgot to mention: The manifold used will be a Crosswind due to $$$$$$
