I have a 1965 2+2 fastback, the vin on the door is exactly the same as the one on the skirt under the hood, EXCEPT that under the hood it has an A FOR the engine code and on the door it has a C ENGINE CODE....Everything else is the same though....I found this strange....Is it possible to have two different engine codes ?  

There is no way to prove if the engine originally was a 2 barrel or a 4 barrel car.  But, if the carburetor is a four barrel Motorcraft with a four barrel intake that appears to be original, then it might just be an "A" code engine.  If the carb is a two barrel Motorcraft, then the engine is most likely a "C" code.  There are folks on here who will tell you that the numbers on the various parts will confirm whether or not it was an original "A" or "C" code, but they are wrong. The door plate could have been changed, the inner fender could have been changed, the individual parts could have been changed to date codes prior to the build date of the car, and if there is no partial VIN on the engine and transmission, then you certainly cannot prove it is a numbers matching car
Face it....you have a classic Mustang built to satisfy the blue collar working American who wanted a sports car they could afford back then.  The classic Mustang was the answer because not only was it cheap, but you could virtually build your own car.
However, in your case, I would suspicion that the door was changed, therefore the new "C" code tag because it is unusual that the inner fender would have been replaced.  To make sure though, take the passenger side fender off and look close to the windshield and you will find another VIN number from the factory.  You can also look at the registration papers to confirm.  

what does the title say A or C code? What ever the title says is what is the car is by law. I would also pull the fenders or go under the car with a light and check the other 2 hidden vin numbers on the top of the inner finder. One on each side. I hope they are both A and you have an A on your title. If not then there could be some problems.

As for numbers matching see the thread below. Most people in the hobby disagree with soaring3 about the numbers matching issue. If you also want to get techinical the carb is an Autolite 2100 or 4100 not Motorcraft.

Could it be a misstamp, yes. Is it likely a misstamp? no  

You can get door tags all over the place, so it may be a repro. If you really want to know, take the right front fender loose and see what the VIN is on that inner fender panel. If it matches to the other fender, to door tag is either a typo or incorrectly duplicated.  

5f09Not4sale:
what does the title say A or C code? What ever the title says is what is the car is by law. I would also pull the fenders or go under the car with a light and check the other 2 hidden vin numbers on the top of the inner finder. One on each side. I hope they are both A and you have an A on your title. If not then there could be some problems.

As for numbers matching see the thread below. Most people in the hobby disagree with soaring3 about the numbers matching issue. If you also want to get techinical the carb is an Autolite 2100 or 4100 not Motorcraft.

Could it be a misstamp, yes. Is it likely a misstamp? no

Motorcraft bought out Autolite, so therefore, you will see a Motorcraft stamp on the carburetors.  And, most people in the hobby includes who?  The two or three on this forum who think an engine with a date of August that goes into an October built Mustang is numbers matching?  

Motorcraft bought out Autolite, so therefore, you will see a Motorcraft stamp on the carburetors.
FoMoCo created Motorcraft as their auto parts division in 1972. This brand replaced Autolite as Ford's official parts brand. So if Motorcraft was not created untill 72 and replaced Autolite then Autolite carbs were used on 64-71 mustangs. I don’t see Motorcraft on my 65 because it did not exist then.

The two or three on this forum who think an engine with a date of August that goes into an October built Mustang is numbers matching? August would be to early for an Oct car. It is not just 2 or 3 on this forum.

Also your statement about there is no difference between a C code vs A code is incorrect. For 1965 the compression ratio of the base 289 was raised to 9.3:1, increasing power and torque to 200 hp @ 4400 rpm. The four-barrel version was increased to 10.0:1 compression, and was rated at 225 hp @ 4800 rpm. Now what did ford do besides just putting on a different manifold and AUTOLITE carb? The pistons and cam are different so there is indeed a way to prove there is a diffrence in a C code and A code, all be it a pain in the ass to do.  

Well I think 5f09 settled that. Soaring, you are a case of a little knowledge gets you into trouble. If answering the question is a bullseye and a close answer is a 9 or 8 ring, you have been shooting the heck out of the backboard continuously. You do provide drama in an otherwise staid forum ,,, lol.