When you're in A/C there shouldn't be anything getting through the heater core and coming out the floor holes. All the air should be coming out of the vents in the dash. Sounds like you might need some new sealing foam gasketing inside you're air box. Another option might be a vacuum problem with one of your door actuators.
I don't have A/C so mine's all mechanical, but I believe the A/C equipped cars used both cables and vacuum to actuate the doors. Not sure if the door at the top that blocks off everything but the dash vents is mechanical or vacuum on your car.
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