If you are referring to the motor gear only turning that far, it should go further. If it only turns a quarter of an inch, it won't open or close the door.
Is it the actuator motor you are referring to?
Here are the directions for removal and replacement of the blend door actuator. I'm adding this just to confirm we are referring to the same part. The attached pics correlate with the directions.
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1999 Mercury Cougar L4-122 2.0L DOHC VIN 3 SFI
Blend Door Motor
Vehicle Heating and Air Conditioning Air Door Actuator / Motor Service and Repair Procedures Blend Door Motor
BLEND DOOR MOTOR
REMOVAL
1. Disconnect the battery ground cable.
Pic 1
2. Remove the glove compartment.
Pic 2
3. Remove the footwell upper trim panel (passenger side).
Remove the pushpins.
Pic 3
4. Disconnect the electrical connector.
Pic 4
5. Remove the actuator.
INSTALLATION
NOTE: When the battery has been disconnected and reconnected, some abnormal drive symptoms may occur while the vehicles relearns its adaptive strategy. The vehicle may need to be driven 16 km (10 miles) or more to relearn the strategy.
Pic 5
1. To install, reverse the removal procedure.
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Let me know.
Joe
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Saturday, January 4th, 2020 AT 7:59 PM