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I had this problem with my 96 Bronco and I took it to a body shop to see about getting it fixed and the guy came out looked at it said to wait a minute went inside got a piece of 2x4 wedged it in the bottom of the door towards the front then pushed the door shut on it and bounced on it a few times. Door shut tight and right for the next three years and was still good when I sold the truck. Guy didn't charge me a thing only took him about 2 minutes. I had replaced the latch but that didn't help seems like a similar problem like the OP said the door seemed to hang down to low to line up with latch. He also recommended spraying the hinges down with white lithium grease the kind that comes in an airessol can and using the straw attachment to really get some grease in the right spots.
I figured out this issue for my dad on his 2004 (I never experienced it on my 99). I loosened the bolts holding the striking latch to the rear door (The non-moving hoop part on the front of the half door). I tapped the strike portion outward with a hammer as far as it would go (Barely moved). I retightened the bolts and it works PERFECT! My dad had asked the dealer on 2 different occasions to take care of it and they said that there was nothing they could do - short of replacing the latches and the hinges.
I had a hard time believing that it was that simple, BUT IT WAS! It didn't even take 10 minutes and the door shuts perfectly (Without using heavy force). It has worked just fine for several months now!
So this is on the door side, not the body side of the truck? I am having troubles visualizing this. You must have just barely tapped it not hit it that hard?
The part that I adjusted is on the Rear Half door (Extended cab) with the front door open and the rear door closed.
It is about waist high (It would be behind the outer door handle from the front door if the front door was shut) and is simply a black steel catch for the door latch and has 2 bolts that require a Torx Bit.
You don't need to remove the bolts, just back them out a few turns. You wouldn't need to hammer the piece either (Unless it is stuck); you could use a piece of wood or something that won't mar the paint to force the catch toward the outside of the truck. Mine moved maybe 1/32". There isn't much play there, but it was enough. I kept pressure on it while tightening the bolts.
Then I checked to make sure that the door latch was still aligned vertically with the catch.
Yes, yours would be different - you have 4 full size doors with pillars between the front and rear, but the principal would be the same - look for the catch and move it outward.
Thanks to everyone posting in this link. Two out of four doors on my 06 crew cab were rattling and driving me bonkers. You guys saved my sanity. What I did was:
Purchase Torx T45 socket bit from Canadian Tire
Find a mallet and a bit of leftover hardwood plywood
Draw a line in sharpie indicating the current position of strike on door frame
slightly loosen the door strike with shiny new T45
use the tapping block to nudge the strike inwards towards the cab
test fit but be gentle; don't slam the door and move the strike (learn from my fail... hence the sharpie start position line)
repeat until the door shuts properly
retighten the bolts to 25 fig-newton-metres (or the SAE equivalent)
This also decreased the crookedness of the door and reduced road noise.
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