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Your vehicle is full of 'front seals'.
Wheel bearing seals.
Brake caliper seals.
Front transmission seal.
Plus a load of engine seals.
At minimum, a full socket set, a full set of open ended and ring, wrenches and a seal pick. Probably circlip pliers.
Google
1992 Ford F-150 replace (which one) seal
and watch the videos.
The usual cause is the dog (gear) on the end does not move out fast enough due to dust/dirt build up.
A clean and lubricate with dry silicon lube will sort that issue out.
Disconnect the battery, disconnect the power cable on the rear of the starter motor.
Unbolt and remove the staer motor, clean lubricate NOT WITH OIL! that will make it attract more dust and reassemble.
Question edited for clarity and typos. 'year make model' in order.
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Passenger side rear bank closest to windshield. See the diagrams
https://www.google.com/search?q=04+ford+freestar+3.9+firing+order
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Perhaps it still is fuel delivery. Isn't there a vacuum in the gas tank? Wind will go in after opening and this happens after a night also.
Another sort like problem is the purge valve, that should be shut when the engine runs or the fumes in the tank are fed to the engine that then could stall running rich. Do you smell un-burned fuel behind the car? See the check and shutting down this hose in the video here on YouTube: watch?v=083JvLiYfGk
Engines need a fast idle and it may be getting colder. This is the automatic choke function. Do check the system of sensors and/or devices that it uses, among the mechanics of being able to push some extra valves open or even keeping the main intake valve closed. Perhaps it is better starting after heating or with starter fluid and you'll find no trouble after riding.
An intake leak check seems advisable. Those short tubes can be hardened and even cracked. Yet it seems that you have taken a good look.
Is in the glass, or the panel trim?
For the glass, they can repair and strengthen it by sucking superglue into the crack under a vacuum like they do for windshield chips. For the trim, they are available on eBay.
https://www.ebay.ca/b/Liftgates-for-2005-Ford-Explorer/33647/bn_92392415
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If replacing the GEM module did not fix the issue, the next step is to check the wiring and connections to the GEM module. Make sure all of the wires are properly connected, and check for any signs of corrosion or damage. You may also want to try resetting the GEM module by disconnecting the battery for a few minutes and then reconnecting it. If none of these steps work, then the problem may lie in the fuse box or wiring harness, and you may need to take the vehicle to a qualified technician to have it checked.
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You may if you wish, try to pull the left side of the bezel out a few inches and reach behind it. You will have to pull it out because the way the headlight switch is clipped in, you have to press some tabs inward and it will release outward. You can unplug the dimmer switch and the headlight switch after its free.
Jan 19, 2010
Question edited for clarity and toss in some CAPS.
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When you changed, or even disconnected the battery, did you reset the anti theft system and engine immobilizer?
The Overdrive light flashing is an electronic issue rather than a mechanical one, unless a solenoid has failed. Thar can be checked by an auto electrician armed with a $5,000 bi-directional scan tool computer. They can instruct all the solenoids to work and verify that they did. There may also be readable DTC codes.
When you emptied the transmission, did you measure the fluid that came out of it and replace it with exactly the same amount?
It looks like whatever the electrical issue is, it is stopping you from driving.
https://www.google.com/search?q=2003+Ford+Windstar+over+drive+light+flashinghttps://www.google.com/search?q=auto+electrician+near+me
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Question edited for clarity.
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Catastrophic failure of something. You need a mobile auto electrician armed with a $5,000 scan tool computer to diagnose the check engine light Diagnostic Trouble Codes and they will tell you what failed and how to fix. It might just be a sensor, but an important one.
https://www.google.com/search?q=mobile+auto+electrician+near+me
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