Sum things to look into are... The Heater control valve along with hoses, and check the heater core for any leaks or clogs...
There's 3 small actuators that control the door flaps, theres one above the gas pedal, one behind the cig lighter assembly, and the last is behind the glove box where the heater core and blower motor are...
In sum cases the flap doors have been known to disconnect and fall off into the housing, so u should check all the gears, springs and such to make sure everythings working properly...
If u want 2 go a step further the best thing to do is remove the dash that in itself is a project... But gives u plenty of room to work with and u can see if anything else needs 2 b replaced...