Acting like one cylinder firing lean.

With an Eddie carb, yes the secondaries should be completely closed but not sticking closed. Depending on the cam, the engine often wants extra idle air. If you can make it idle so that the mixture screws are sensitive, with the secondaries fully closed,then you possibly don't have enough idle timing.Make sure the secondaries are not hanging up for other mechanical reasons, like a displaced or wrong gasket,etc.
If your brake booster supply hose runs off the same leg as the problem cylinder, well you better look into that. My intake did not like that plumbing. I replumbed the booster hose to the back of the carb, but I had A Holley DP. That cured it. You may need a new checkvalve on the booster.