Forgot to mention it's also through the stock throttle body. In his situation, the plenum is the bottleneck so changing to a better flowing manifold/bigger throttle body would probably result in a big increase of power straight away. He decided to start again with a new engine as this one was getting out of hand, you can't buy off the shelf plenums for RB25DE's that we have found.
But if you aren't AT the bottleneck yet, I don't see any significant gains other than being a bit more free in the top end.