The amount of air passing through the carb at idle is significantly less than that at 35% throttle. Gut feeling tells me that even with a screwed up idle circuit, that's probably not the smoking gun.
Often, aftermarket exhausts combined with different air boxes / filters can be a real bear to jet correctly. I had some serious surging issues at cruise RPMs when my jetting wasn't sorted out, and I bet you do, too.
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