Side cargo door does not close tight. How do I adjust it?

The latch striker may be adjusted just a bit too tight. What is happening is that when you attempt to close the door, the air pressure inside the vehicle resists the door closing. That is why opening a window solves the problem. There is no back pressure to fight the door closing. If the latch is adjusted properly, then you just need to put more oomph into closing the door.

Your door ajar system is tied into the door latch mechanism. if the door still appears to close tightly, and the door latch works properly, then you may need to adjust or replace the latch, though ford has listed a cleaning procedure for the latch that involves using a tool to test latch position and manually closing the latch (while door is OPEN) using a screwdriver 10-20x and monitoring to see if the latch consistently shows CLOSED and OPEN when it should.
If pushing the door closed after its already closed causes the lamp to turn off, an adjustment of the latch may help, or cleaning the latch contacts may also help. If the door never shows latched regardless of how hard it is pushed, it may be a defective latch, or a wiring problem (Door wires sometimes break in the door harness between the door and the side of the dashboard when the harness enters the vehicle).

remove the door trim to get to in side the door. One of the glass tracks will have an adjustment on the lower mount where you can move the track in or out depending what you want. Normally wind the window right down and adjust the track tight against the glass( make sure the glass is in straight). wind the glass up and down a few times to ensure that there are no tight spots Some spray silicon in the tracks helps with the movement of the glass.

Power Door Locks Circuit Description
The power door lock system incorporates door lock switches on both front doors and on the RH D-pillar, door lock motors in all passenger doors and in the RR cargo door, a door lock relay and a door lock control module.
Power for the door lock switches and the door lock control module is supplied from the CIG LTR fuse 13 through CKT 640 (ORN). Power for the door lock relay is supplied from the PWR ACCY circuit breaker through CKT 540 (ORN). Ground for the door lock relay is supplied from G202 through CKT 150 (BLK) and ground for the door lock control module is supplied from G400 through CKT 150 (BLK).
The door lock motors are reversible and both sides are connected to the normally closed contacts of the door lock relay. Those contacts of the relay are connected to G202. When any of the door lock switches are placed in the lock position, voltage is supplied through CKT 195 (LT BLU) to the relay lock coil. Since the other side of the lock coil is connected to ground, the coil is energized and it pulls the lock contacts closed. Voltage is then supplied through CKT 295 (GRY) to all the door lock motors and the doors lock. The unlock function operates in much the same manner except that when any of the switches are placed in the unlock position, voltage is supplied through CKT 194 (WHT) to the unlock coil of the relay and CKT 294 (TAN) supplies voltage to the apposite side of the door lock motor and the doors unlock.
Door Lock Control Module Description
The door lock control module is used on vehicles equipped with cargo doors. The purpose of the module is to lock the cargo doors after a lock cycle has been commanded from any of the door lock switches with the cargo doors open. When the RH cargo door is open, the module receives a ground signal from the closed contacts of the rear door jamb switch on CKT 1897 (ORN/BLK) to G400. When a lock command is received, the module retains this input until it receives an open input from the rear door jamb switch. Then the module sends a lock command through CKT 194 (WHT) to the door lock relay and the doors lock.
Rear Cargo Doors Description
The power door lock motor will not operate unless the rear cargo doors are fully closed. The power door lock motor is in the right cargo door. The contactors are on the rear cargo door opening on the body and on the right cargo door.

I don't believe the window issue is related to the door adjustment. But the interior lights flashing are> It would be the same instance if you were opening & closing your drivers door while driving. The rear door isn't closing tight enough to shut door jam switch.

The seals allways let some in, I just looked and mine has 4 3 or 4 mm holes to the rear emptying into the rocker panel. If you are worried about the lower rubber do a pinch test with some A4 paper, close the door with a sheet of paper held where the seal is and when the door is closed see if it is held, check somewhere you can see better to find how hard it pinches. I do not reccomend adjusting anything as if the lines are correct it must be right and they are none to easy to put right, I hope this solves it for you.

need to get a body man to adjest it

if you look at the latching mechanism on the bottom of the door, you will see two metal teeth. If they are close together, you will have to have somone hold the handle like they were opening the door and use a screwdriver to seperate or open the teeth. Then you shold be able to close the door. Hope this helps :)

check your door bushings in the door hinge these probably need replacing. if you can lift up on door and feel play they are wore out. common issue on these if not you can put a wood block betwwen bottom of door and body and push on top of door to bend it a little to close top tighter

pull the outside handle and unlatch the latching assembly by hand by insertins a screwdriver where the striker would normally be if the door were closed - and pry out.

You can adjust the striker by loosening the bolts, and moving it in toward the cabin.

If the door itself is droopy, adjustments are made by the hinge by loosening the bolts and lifting up or down.

Multiple attempts will be necessary to get it just right.

Dont get frustrated if it doesnt fit properly in the 1st or second attempt.
Good Luck!!