No brakes in the morning. It will definitely wake you up more than coffee.

[WyrTwister]

The engine ( green ) is pulling air in , past the throttle plate ( yellow ) . This restriction , by the throttle plate , results in a vacuum in the intake manifold ( Blue ) .

The climate control ( brown ) does use vacuum from the intake manifold ( blue ) .

As does the brake booster ( red ) .

This diagram does not show any check valve in the brake booster system . It may have one built in ?

Until you get the problems corrected , I would make it my SOP to get into the car , start it & pump the brakes until they are OK , before I put the car in gear and drove off .

The valve cover and connecting hose ( purple ) I am guessing represent the PCV system ? I think you said you worked on that ?

The vacuum tank may or may not have a check valve in that system ? Check the tank for cracks / leaks , also .

The last major system I see is the evap control system . You could also have leaks there or valves that are not opening or closing properly .

God bless
Wyr