The 41a's I have do not have an external vent hose like the 42b's or pd's on my wife's cb650 for that matter, from what I can tell they vent through the overflow tube in the float bowl. Try setting the float level with a caliper and don't check it with the clear tube, see if it overflows or not without the tube attached. Possible that with the clear tube attached to the drain of the bowl it's not allowing the atmospheric pressure to equalize in the system. That's the only theory I could come up with. If you find that stops the overflow, you'll just have to trust the float level is correct with the caliper and not worry that you can't clear tube check the #2 body. Every other set of PDs I've looked at have a vent hose externally, my 41a's don't. Interesting that you have the same issue with the same set of pd's.
I completely cleaned my carbs and I mean clean... New oem gaskets & orings, new jets, new floats & rubber tipped float needles. Manually set floats to spec, double checked levels via clear tube. I manually checked my floats and needles shut off fuel flow with the bowls off, I never could figure out why it was overflowing. If I swapped floats and needles from carbs 1,3,4 the issues stayed with the #2 body. Oddly enough the issue stopped when I switched to the 42b bodies, which have an external vent tube as part of the venting system. I cleaned the 42b bodies and put all of the 41a internals in them. No more overflow,