Engine Surge While Stopping

Zelus, sorry if i misinformed you i was referring to the butterflies at the bottom of the carb, the secondary butterfly plates are mechanically linked to the primarys and they should open and close freely with the linkage, the upper plate on the secondaries is counter weighted and only opens when enough vacum is created when the throttle linkage opens the lower plates. I'm pretty sure this counterweight/vacum opening system on the upper butterflies is non-adjustable or at least not user friendly to do so.
Maybe one of the more knowledgable people will confirm or correct me in this.

But sounds like you were onto to something with the linkages, or perhaps the accelartion pump needs to be adjusted, if i remember right there are 3 differnt holes to adjust the height/shot of the pump, just throwing things out there. I do as 73AbodEE suggested and try another carb and see if it fixes it, (would at least get you pointed in the right direction) or maybe give yours a rebuild? I know you said it worked fine before the intake swap just dunno why a vacum leak would come and go like that