I would think the rod from the key cylinder to the door lock mech is off or broken.
These are pictures from when I put the keypad on my 2001 SuperCrew. The mech could be slightly different, I do not recall if this is different on the SuperCrew vs the SuperCab or Std cab trucks.
Viewed through the door panel opening ( key cylinder already out, you can see the opening rod is straight up by the red )
You can see the rod connected to the key cylinder in the upper left of this picture, down to the door lock. This is what you need to check.
Close up of the rod attached to the cylinder
This is a better shot of the key cylinder. The spring clip is removed from the cylinder, that is why it is free in the door. Take note of the way the rod attaches to the cylinder. This is plastic and could be the cause of your symptoms.
This is where I would start considering the door works as normal with the power locks both inside and out.
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