I know you said the carb was clean....but I will bet dollars to donuts it has a small piece of crap stuck in one of the air/fuel passage ways. Soak it in pinesol for 24 hours with a shake halfway through, just the metal parts, no diaphram or slider plus no smaller diaphram off the side of the carb, but everything else. Wash off the pinesol with hot water, then use spray carb cleaner through all air/fuel passage ways to make doubly sure they are clear, then again blast all air/fuel passage ways with compressed air.
Set the needle if a KLX needle kit at 3rd clip or middle slot, use a 145 main jet, set the, damn pilot jet under the cap at 2 1/4 turns out from seated...I hope I have the correct name for it, for some reason it isn't sounding right, sorry, head is a bit cloudy, you know the one I'm talking about.....augh! Check every jet and brass tube for complete cleanliness before installation and no holes plugged. The holes in the top of the carb are fine to leave there. I set all of the bikes here at that setting and they all run perfectly, I'm a stones throw away from Toronto so to speak elevation wise....so if you are the same elevation this setting will work well for you. Make sure your air cleaner is clean and oiled correctly also. Put in a new spark plug, I use Iridium plugs, yes I know not needed but they do work well. The plastic choke thinga ma jig has 4 tangs on it and if you have snapped one it may be causing this issue but I doubt it. There is a alluminium replacement for it from Stead Engineering...it's a bit steep cost wise but it's perfect.
Hope this helps as a starting point from which you can fine tune from.
Plus I hope it's understandable.
Oh you must use stock jet numbers and not Dyna Jet numbers for the main jets etc as they do not use the same scale for their numbering of the jets, just to confuse the rest of us for tuning.....the main jet numbers I gave are the stock jet size numbers not the DJ number .