I measured both manifolds, these are quick rough measurements. The flange where the throttle body bolts up is actually the same height. The portion of the manifold where the center brace of the hood is is about 11/16" lower and the rear (box) portion is a good inch lower. It sure looks a lot lower than that and clearance to the hydro boost is much better as well.
I'm using an Explorer throttle body turned sideways (throttle linkage down) with what I believe is a Crown Vic IAB (super short) nothing is above the flange on the intake manifold.
From my guesstimate you could add a WH integrated 1" body lift, use the tubular GT-40 manifold and add a 1/4-3/8" in body washers to the body mounts and be good. I have a Windsor waiting for a stroker kit that I will be installing some day. I refuse to cut my hood OR run a 2" body lift.
Good stuff right there ^^^^ Thanks needabronco!