Can somebody explain to me the thermodynamics diffusion and laminar flow equations that led to Toyota engineering putting a diffuser screen and the intake plenum?
No idea (of even whether it is about thermodynamics diffusion or laminar flow equations or for some other purpose entirely), but there has been at least one other thread posing the question.
The funky grid is part of the throttle-body gasket. But notice how the manifold has some cutouts where the tabs of the grid have to go. The original manifold hasn't got those cutouts, and the updated throttle-body gasket won't fit. The updated manifold that was introduced in a TSB has the cutouts. People have run into this when buying throttle-body gaskets. The non-griddy version of the gasket will fit either manifold, but the griddy version only fits the updated one. What the grid is good for in a throttle-body gasket hasn't been answered yet (here, anyway, that I know of). But grids turned up in a lot of cars' throttle-body gaskets around the same time. Maybe someone can find what the engineers were all talking about around that time. There's an older thread around here somewhere with all this info on it.
Slightly downstream, but tucked off in a corner, the manifold absolute pressure sensor. Waay downstream, the A/F ratio sensor and oxygen sensor....