Yeah just remove the TB...
As far as porting and polishing... Biggest enemy is heat, so I wouldnt go overboard on the polish part, might end up with a cracked plenum.
The lower plenum shows a huge difference if you shave down some of the runners... I've done it, and with a spacer and bolt on Mrev i did see a difference...
here is a really good write up on how to do it... I suggest reading the whole deal as there are big differences depending on how you modify the plenum...
http://my350z.com/forum/engine-drivetra ... rting.html