Not sure on the intake manifold manifold side of things. The stock exhaust manifold is pretty restrictive though. I had it off when my head to manifold gasket went. My mech heavily ported cyl 3 runner to get it close to what the others were flowing and also needed to port match between exhaust manifold and the turbo where there was a decent step up or down - can't quite remember. Seangti went from an aftermarket exhaust manifold back to a stock ported one I think and still lost some power I think so there is a fair restriction there. The restriction is probably less of an issue with the stock ko3 but if your going to a hybrid or ko4 like he did then it may be holding you back measurably.
I'm not denying there is an issue with head to manifold heat soak after you park the car but I woulnt obsess about it. The issue is if you've been hammering around and then stop for a feel and the manifold is hot then. Your ic should be keeping it cool when you're underway yeah? Try insulation wrapping your ic to throttle body hose to prevent heat soak there. As long as your throttle body is cool to touch, you know your induction air is arriving at the plenum cold. It should move out of the plenum pretty quickly without picking up temp from it since its a large body of mobile air.
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