My guess is something to do with the pulse generator or cdi., mostly the cdi. They have a tendency to do goofy thing when they get hot, then cool down and work good for a bit. As for running , even though crappy, till you idle it down then puking it definitely sound s cdi issue. Most of these cdi have 2 advances, one at 8-12BTDC for starting(low rpm) and then switch to 28-39BTDC(depends on brand/model/year). As they fail sometimes one advance quits and it'll run, somewhat, on the other. In this case it sounds like the start advance(low rpm)has quit and the normal one is failing as it heats up.
Try tapping on the cdi when it acts up to see if anything changes.
My other guess is the pulse gen not sending all signals when it gets hot.
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