[84LX89GT]

I've heard that when you port match things, basically what you do is scribe a mark around the hole where the gasket is (depending on what type of gasket). If it's the new style with rubber sealing o-rings, i'd scribe pretty much at the port hole, if it's an old style gasket (plain looking, silver), then i would probably leave 1mm or so until the gasket all the way around. The key is just matching the sides together and blending the match about 1" or so into the cylinder head and intake manifold. If i were you i wouldn't polish the lower intake manifold because since it's right before the fuel injectors you want a little bit of turbulance to pick up and swirl around the fuel so it doesn't get stuck to the port walls or pool anywhere. Using a fine grit sandpaper cartridge for the lower intake is what i'd recommend as an end finish. If you wanted to and had the time, polishing the egr spacer wouldn't hurt (although i'm not sure if it's rough at all to begin with, and the throttle body you probably should just clean out with a throttle body cleaner (although ford doesn't recommend this because of the Teflon coating, all the throttle bodies ford makes gunks up anyway so Ford is smoking something funny).
While you're in there, you may want to gasket match the exhaust side of the heads and grind down that enormous thermactor bump flush with the port. Polishing the exhaust would possible help as well.
I'd say if you're putting an intake manifold on stock heads like i did, gasket matching/very light porting should be worth at the very minimum 10-15 horsepower because of the differance in port sizing especially on the intake.
Good luck,