I do have the heat flapper tied to block off the intake, so I know that isn’t helping but I’d rather keep the intake cooler once hot (if that makes sense)
That's a pretty complete (and pretty common) misunderstanding of what intake manifold heat is for. That valve setup was put there for good reasons having very little to do with how cold or hot it gets where you live. You might want to try restoring the correct function of the heat control valve. Not only might it alleviate that cold stumble, but it will also make life a lot easier for your engine in terms of reduced wear and longer engine oil life (significantly reduced gasoline-dilution of the oil). Easier for your wallet, too, in terms of improved fuel economy. And you might be shocked to find improved driveability and performance, too.
The 5041 is all kinds of nifty. The original linkage kit works well (with some cleverness, as you found) in the pre-'67 cars with the rotating-rod throttle linkage. Choke setup/hookup with the dual 1bbl intake is almost-lost knowledge; see here.
