The modulator line should hook to the manifold, not the carb. I have never seen a manifold that did not have a vacuum port somewhere, so it might be capped off. What kind of manifold is it? If you have a brake booster, you can use a T-fitting to tap into manifold vacuum where the booster line connects to the manifold.
Bear in mind that I am not familiar with Holleys (I stick with Ford carburetors), and am not sure what that myriad of ports is for. I am only sure of the way Ford intended for it to work. If there is a way that Holley intended to run the modulator off the carburetor, I am ignorant of it and have never seen it, but that doesn't mean it can't be.
'65 Coupe, 302, Autolite 4100, C4, 3.00