2011 CX-9 driver door handle and window motor questions

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2011CX9 Touring
My driver's side door handle and window motor failed in the spring so finally getting around to fixing it now. I have some questions before I finalize this fix. The door handle was replaced and use old lock/keys combo. I have the interior panel still off and have some questions to finalize this:

1. when I raise the window when it is more than half way open the window will go all the way shut and instantly lower if I hold the window power button in "up" position. The window is properly aligned now. New motor appears to work fine. Do I need to reprogram the window motor so it will shut and not lower immediately? I fixed the front passenger window and if I push up on the motor it goes all the way up, shuts, and stays shut. If I inch the window up on the driver's side it will shut. Problem occurs if I hold the button in "close position".

2. When I enter my key into the driver's side keyhole nothing happens. No clicking. seems like something should be attached but isn't. I attached to two levers to the car handle from inside the door. The key fob can open and close all doors with no problems. There are two wires that are associated with lock/lock. The white plastic tip one if I pull the door opens no problem from the inside. If I trigger the unlock/lock on the key fob I see the black tipped cable moves. This situation is my biggest problem since if there is an electrical failure or dead batter I won't be able to unlock my car.

In the attached picture I dont' have those cable for door lock attached to inside door handle lever (in red circle). Is that causing this? seems like the issue would be something else.

Thanks!
 

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One last issue is after I took off the door panel from driver's door occasionally when I step out the vehicle with key fob in my pocket I hear the door mechanism activate and then the driver's door rolls all the way down and moonroof opens up. In my 10 years of owning this vehicle I never seen that happen. I'm unable to replicate this action intentionally but it happens ever couple of days the week I've had panel off. What is causing this?
 
One last issue is after I took off the door panel from driver's door occasionally when I step out the vehicle with key fob in my pocket I hear the door mechanism activate and then the driver's door rolls all the way down and moonroof opens up. In my 10 years of owning this vehicle I never seen that happen. I'm unable to replicate this action intentionally but it happens ever couple of days the week I've had panel off. What is causing this?
You can do this with the fob. Something like press unlock 2 times then hold to open the windows. Both fronts should lower. I only messed with mine a few times. Sounds like maybe the security module is acting up.
 
Well all seems fixed now. So going back to my problems I resolved:

After installing windows I need to reprogram the window motor. Need to program passenger's side and then driver's side so switch learns placement of window I guess. Didn't know that until watching many videos.

WhenI was doing the window I did not have window all the way up and it fell out of place fromit's groove. I think before I placed it back into it's grove it knocked the lever that attaches to keyhole. There are 2 of them and they got knocked out a couple times until I could keep window up and in it's groove. been testing door for couple days and it seem to work fine now. The lever that is loose is activated with key physically in key hole. This could have probably been avoided if I did everything with window all the way up.
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