The tubes sticking up from the floor of the intake manifold are the EGR delivery tubes. Clean them out with a piece of stiff wire....they shouldn't be full of carbon. Just rod them out so the EGR can flow properly.
Clean the throttle body bores and the back side of the throttle blades with carb spray and an old tooth brush. Disconnect the battery negative cable for 30 seconds when you do this to reset the idle learn values in the PCM... As the deposits clog up the air flow around the perimeter of the throttle blade the idle speed control has to open the throttle further and further to establish the correct idle speed and it 'learns" this offset from normal. Cleaning the bores and blades will re-estbablish the correct air flow for idle and the learned values need to be reset with the battery disconnect so that the idle will not be too fast at first.
Port fuel injected engines with "dry intakes"...i.e..no fuel in them...all the fuel is injected at the intake valve...typically get very "dirty" from the soot in the EGR gases and the slight oil mist from the PCV that is introduced into the system. Pefectly normal. Carbs and TBI systems with lots of gasoling sluicing thru the throttle body/intake stayed pretty clean....gas was a good solvent.