So before I get ahead of myself here, lets get a little clarity.
The ignition is good, plugs, points, caps etc.
This is a rack you built from 2 different sets to create 1 good set. Correct.?
If that's the case you're going to have to look a little closer at the entire carb rebuild and
reassembly process, as it's described now your issue sounds like a dirty slow jet or slow jet passageway in the #1 carb. That it improves as it warms is a pretty good indicator of this, as the engine warms, a slightly lean enough condition in the slow speed circuit will enrichen just enough to fire once its hot.
The issue with it developing a hesitation once it warms up indicates a rich condition overall, double check your float heights (level). Make sure that you've got good brass and their accompanying o-rings and make sure your needles are in the proper position.
Then if all of that is good, double check you sync, if its off enough your #1 carb problem could be there, however if its that far off you ought hear quite a bit of primary knock regardless of temp.
Small carbs like these can be quite sensitive, so everythings gotta be clean and properly adjusted to function as it should.