Mis-Matched Numbers

someone changed the door at some point with a door form an C code car the vin on the fender is the correct one.

did the numbers after the A and C match?

In that case I would think that one or the other was mis-stamped check the one on the passenger side as the tie breaker. It is harder to get to as it is under the fender but that will give you confirmation. Also you can look for a build sheet under the carpet or tied to the under dash wiring harness the build sheet is a long shot but worth a try. you can also look for a body buck tag but I do not know where these where located on the early cars.

There are also places that will restamp the door tage for you but I would not think that some would go through the trouble of getting on and installing it with the wrond number.

That happened a lot on the assembly line. If all the numbers, except the engine code match then most likely a worker on the line mis-stamped the door tag or body VINs. From your description I bet the body VIN was mis-stamped. Jester67 is right, check out the hidden VINs under both fenders. Loosen the bolts of the driver side fender and you should see the VIN (its to the right of the visible VIN) and see what it has. Do the same with the passenger side. If all the body VINs show an A code, and you are sure you have a C code rear axel (2.80), then it looks like the factory decided to change your car to a C code at the last minute, or a worker caught the engine mis-match and just changed the door tag. Mistakes like these were actually very common and MCCA judges know what to look for in those cases. As for adding value, it really doesn't and some people get very leery about buying cars with mis-matching numbers so value can actually go down. True Mustang collectors would realize this though and they may actually consider that a plus. It's all up to the individual. If it was me and I was concerned about originality I would keep it as is. But if I wasn't I'd swap in an original 4BBL and intake and have fun with it. I'd keep the original intake and carb though and leave the door tag as is in case I decided to sell it later, and I'd tell the prospective buyer the true history of the car.

The body vin is the "Gospel" as far as registrations is concerned. No matter what engine you have, (unless the other two hidden codes are "C") you have an "A" code car. As the others have mentioned there are lots of cases of mis-stampings.