I think the 4100 AF-DG isn't the correct carb for a 289 HiPo, though it probably doesn't matter a lot unless it's a concours car. But I believe that carb was originally an auto choke unit and may have been changed to manual choke. Makes me wonder if it doesn't have some home made linkage that's screwing it up. With the exception of the rod going to the choke flapper, my 4100 has no brass parts of the choke linkage. Everything pretty much is gold cad plated steel. That also makes me think home made. Could that be what's going on?
As far as the check ball for the secondary diaphragm, I'm not sure. I've seen 4100's with and without. I think they may have dropped using it depending on the size of the secondary vacuum port but I don't know enough to say for sure. These are the people you want to talk to about it:
Carburetor, Carburetors, Carbs, Carb Parts. Pony Carburetors - Your Ford Carburetor Restoration and Part Sales Specialist
Larry