I’ve never had the problem you’re experiencing and I’ve run a pump-around for the last 3 seasons on my Honda. You’ve taken care of the rebuild, so my only other suggestion would be to check the tank vent line to ensure you’ve got an open line. Also changing your fuel filter if you haven’t already.
You mention heavy springs in the clutch. As in heavier than stock? My Honda is the easiest of the three motors I’ve had to launch (Suzuki RM125 and TM Moto). The clutch should be smooth to engage and disengage. Maybe try a different gearbox oil? I have tried several and the Royal Purple made a huge difference mid-season this year. Of course it will take some practice to be consistent, but she should be able to get there early next season. Learning to grab the clutch and/or keep her foot in it during a spin is another area to learn to not stall.