I think you are afflicted with a classic problem with using multiple carburetion - too much carburetion at idle. When you have multi carbs the idle speed races - to slow the idle speed you close down all the throttle plates - doing this richens up the idle airflow, since the idle circuit tends to richen up as the plates are shut the overall A/F ratio at idle is too fat - OK for a cold engine but at operating temp it will be too rich.
You must find a way to lean out the idle circuits. On Holley 2Vs this is done by idle transfer slot modifications and idle air bleed changes (usually necessitating changing to removable air bleeds ala racing carbs). Kind of tricky but a good carb blueprinting shop should be able to perform the needed mods. I'm not real familiar with Model Bs but this is what I have learned playing with (3) Holley 2Vs on my junk.
