Well I have the benefit of my old man who used to be a mechanic to help me. My main worry would be doing it and messing the engine up or worse distorting the engine due to it, I know that sounds extreme but you gotta take all things into account when doing stuff to the engine as I would be altering the air flow rate and as you say Andy, most places would probably use some kind of air flow bench, but in the same vain I can't see Toyota/yamaha really spending to much time making sure the plenums are as smooth as can be and being caste unless you port them you will always get imperfections on the tunnels, could explain why some 3s-ge's feel slightly quicker or get slightly better results as the caste was smoother when it came out the machine, again just a theory of course.
And on another note, my car has done 152,000 miles so I can imagine the tunnels on the plenum are not as smooth as when it was made, and it wouldn't surprise me if it also had oil in it too