[rated ///M]

Take off the manifold and check all your vacuum lines under there and the plastic L fitting (located between 2 vacuum lines). I would also get a new intake manifold gasket and replace it while you have everything apart. Take off the ICV and twist it side to side, the metal flap inside there should move freely, if it doesn't use some carb cleaner and spray it in there while moving the flap up and down.

 

[rated ///M]

Also you said you replaced the MAFS 100 miles ago, make sure the intake pipes aren't kinked on the bottom and creating a vacuum leak. Sometimes when you tighten down the clamp it squishes out the gasket on the bottom creating a leak.

 

[rated ///M]

Is the intake manifold gasket the rubber boots at the bottom of the throttle bodies? Speaking of which, how do you clean the throttle bodies since I plan to take off the plenum and do a full scale cleaning/vacuum leak check.

No it's the upper one that goes around the plenum, part number 11 61 1 406 657. Just take a rag and wrap it around a screwdriver and clean it while holding the TB's open.