i consider polishing the port runners on the intake manifold of a throttle body injected engine to be counter productive. the injector fires directly into the floor of the small plenum on those manifolds where the fuel puddles and largely requires the heating of the manifold to afford vaporization.
the inducted air/fuel mix benefits from irregularities on the runner walls to perturb the air to help the mixture. polishing the walls gets rid of that.
i don't mind a little work to knock down big casting peaks or a little effort to port match but i always stop with a final finish of 80 grade sandpaper on the port runner walls.
a little polishing on the exhaust side is okay, it helps to keep carbon from building up in the ports and you want to keep gas velocity up on that side. still, all in all i've seen little in the way of huge performance gains just from that work. on the 3 banger, it seems that the cumulative effects of all the little tweaks improves performance but it's hard to put any single thing ahead of another on the list.
so, my take on polishing the intake manifold is that the time is better spent on something else. get a 3 tech performance cam, improve the exhaust system, remove the air filter bridge and install a less restrictive air filter system, install an aluminum under drive accessory pulley, install a flywheel and clutch from a g13 (and lighten the flywheel if that work is in your budget.)
my 2 cents.