That whole intake manifold design is just a mess on the 3.8. When I look at Ford's later Vee design engines ... such as the 5.0 V8... I almost get mad over the improvement.
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Anyhow, we have what we have, ... if I were to explore the scheme of shutting of the flow; I think I would just remove the lower intake manifold and explore the chance of cutting female pipe threads into that tubing hole. If that works, one could explore just using a flush pipe plug .... OR, using regular pipe fittings ... go immediately to hose and get ride of tubing. All depends if there is vertical room for such.
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.... you could always go by a shop that does head repair and get the hole plugged up with weld as a fall-back plan.