All you need to remove is the tb and the upper intake manifold.. Just fit the itb to the lower intake for the time being. i see that you recessed the itbs into the lower intake manifold.. But that 1/2" or so wont be that much of a diff to get things figured out for spacing and a plenum placement/ design. And it will save you a little time and stress if you dont have another car to drive.
Im already thinking of another design...