I hope the attached picture is clear enough for you to see. As the caption on the picture states - There are a surprising number of potential spillage sites on an induced draft furnace. Basically anywhere there is a connection, joint or hole. Burners are the largest hole. Combustion gases can exit out past the burners rather than continue their path up the heat exchanger and out the intended flue vent.
Monitor the pressure in the vent, if its positive in the vent for more than a minute it is most likely backdrafting.
Use smoke at the hole you've drilled to take your CO measurement.
When sharing a vent with a water heater check for spillage at the water heater draft hood.
I've never had any luck determining spillage at the base of the flue as theres a lot of moving air there from the inducer motor.