The choke circuit works independently to the rest of the carb jets. You've confirmed fuel in float bowls, so you either have blocked choke jets or the ignition is playing hit and miss. I'd certainly expect the bike to readily fire up from cold. The vagaries of 40 year old electronics & known frailty of old HKZ black boxes should not be ignored, as Lee's experience shows!
Not sure what you mean by "stalls from idle when cold" If you crack open the throttle without any choke, I'd expect that...especially if those 55 pilots are still in there.
My usual Dell'Orto starting procedure on triples & twins is apply full choke, no throttle, crank the engine and back off the choke half way when it fires. The choke can usually be pushed fully off 10-15 seconds later. If working correctly, tweaking the choke lever will regulate engine speed after a cold start ... no need to touch the throttle.
Operating the throttle when cranking from cold with the choke on will negate much of the choke circuit operation because the vacuum created by a closed throttle slide is lost. HTH