as far as clearing the hood, i don't have to worry about that as i am mating to the lower runners. i come to the conclusion that i will have to tapper the rear of the plenum to make room for the brake booster. But that seems like an easy fix. The manifold will look similar to the one made by some of the high dollar company's at a DIY price.
Look and perform will be two different things. This is actually the same exact setup that First State Motorsport produces. They use the RMR D plenum and drill here and there to work with the lower runners. I am going to assume that you too are using the RMR plenum as they seem to be the only place to get them. This intake setup works fine, FSM or The Quickness from Supra Forum had the intake setup flowed by Head Games and there was no sign of any air flow change in the design.
Again, can you explain what this setup is for? An IS? SC? GS? You keep on asking about a IAC flange, when people keep saying the IS300 don't have one. Also what engine management will you be using? Converting into a non dbw throttlebody will mean you will lose cruise control and the idling controlled by the stock ECU. I think you should explain or give a little bid more detail on you engine and/or turbo setup.