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Yes, all A codes came with a Motorcraft 4100. If that Holley is still working for you, I'd just keep it on and keep using it. Less than 600 cfm is good to go. The 4100 has something like 480 cfm.
Yep its a small and it will work just fine on a 289. Those carbs were on alot of engines, and they were also sold as stock replacement carbs. You wont get super great mileage with it, but it will run nice.