I saw someone post this exact question on a FB S type page but the responses were obvious jokes. with the windows up, I hear a distinct thump coming from somewhere near the glove box and passenger door but everything seems light

whats that thump I want to fix it

 

I know there are air vents in the trunk just so the air blasts from slamming the car doors can escape. But I have never seen any vents up in that area?
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may be the fresh air/recirc door reacting to the pressure of windows closed and door being shut. Check it under the glove box that it is held by the actuator

 

Scottjh9 Thanks for reminding me of that!
On my old 2003 Lincoln LS I had the same noise but it was so long ago I had forgot about it?

On my LS it was exactly that fresh air/recirculating door. What had happened was the plastic actuator arm broke the connecting piece off the blend door where it attached to the blend door. I never could tell any difference in the heating and cooling? So when the doors were slammed this door popped up and fell back down causing the clunk noise. The fresh air door itself lays horizontal and is pulled open by the actuator.

What I did was lay on my back on the passenger side front seat floor. Feet and legs over the seat back - yes it's real comfortable! Remove the soft trim under the glove box and you should be able to to see the blend door. Push on the door to check if it's floppy and to be 100% sure that's the noise have someone slam the drivers door while you watch the blend door. You can also start the car and cycle the climate system thru all the positions and you should see that door open and close as commanded by the AC system.

Now for the bad news IF that is your problem. The actuator is not too expensive and a used one would be fine as this is NOT a common failure. The problem is the dash has to be removed to get at the blend door. A HUGE amount of work. Now for how I fixed it. The plastic can't be glued together as it just won't hold. There is not much room down there either. I drilled several small holes in the two bits of plastic and wired them together.

Here is the actuator. On mine the arm was intact but where it attached to the blend door was broken. The actuator can be changed it's just a bit tight to do. The blend door is something else!! If needed the actuator is part #XR857888 about $60-$70.




Here is the best diagram I can find in the JEPC which does not show how these things go together very well at all!!



Item #14 is the door that I think is making your noise but it's just kinda floating out in space in the diagram so it's of little help. This is the part that broke on my LS.
Part #XR83700 does not look to be in stock and is about $110

If you can let us know if our guess's are helping any??
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You can also see the blend door from the outside by removing the cabin air filter under the windshield cowl

 

I dont have to look. I know youre correct because I thought I had fixed a few years ago. I guess my fix failed.

 

OK I did not realize you had fixed this before. I don't remember you posting about it but I know you did a boatload of work to your STR when you first got it.
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ya I made a post where I epoxied a washer on the door attachment flange. I thought it would hold. Dammit. It was a few years ago right after I got it