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what kinda carb do you have? was any work done to the carb? have you checked the floats if it has them? i say this cause mine did the same thing after a rebuild was done to the carb when i got it and the "mechanic" who did it left the jet screw loose
double check the carb to make sure that the needle's didnt get outta adjustment, might just consider doing a rebuild on it. a rebuild on a 650 holley is simple. but what it sounds like to me is that when the carb and intake wsa removed the needles was thrown off. its a quick and simple adjustment if you know this style of carb.
its simple, you have 2 screw in front and 2 int the back. one of them is on top and 1 on the side. get some gas pumped up in the carb, and remove the screw on the side (which is really short by the way). now release the screw on top and turn the nut thats on it until gas is just trying to come out the threads on the side. tighten the screw on top without allowing the nut to turn replace the screw on the side and repeat for the back.