In the same position with CRD. Only just coming through, no tech info and not much in the way of coarses.
Not to sure if I understand your question correctly. But in my understanding (I could be wrong).
The throttle plate only works under certain conditions start up - to reduce the amount of air being compressed, shut down - to reduce delta 'n'(?) which is the speed up and slow down of the crank during shut down - reduce vibration, also to increase manifold vacuum to aid EGR flow. Probaly many other conditions I'm not aware of.
As for cleaning the manifolds, I would say yes. Toyota with their EGR problems on the SR5 Hilux is new manifolds and plumbing including EGR cooler (which, I am told, is redesigned) if still under warrenty. If out of warrenty, a clean of manifold is offered - no guarentee's.
This will also apply to the SIDI which is apparently based on Mitsubushi's GDI which uses huge amount of EGR - bad combustion (bad ignition) leads to massive deposits in the intake tract that interupts swirl of the incoming air into the chamber that makes for more poor combustion.
As I said, this is only my understanding and limited experiance.