The car does not have the original engine or transmission. The body numbers on the radiator support and the trunk lip match the order number on the trim tag. I emailed the curator of the Super Bee registry and he confirmed it was a very early build as well.
When you have something that is out of the norm, it's best to have rock solid documentation or a plausible story. Let's see if we can determine what you really have.
You have a car that was, supposedly, built 4-5 months early than what it should have been.
That will raise a lot of questions.
I would think the first person to raise a red flag would be the 'curator' of the Super Bee registry.
It has a non matching numbers drive train so one way to tie together everything is missing.
If this is an early production car, why was it built at the smallest, lowest production, furthest away plant instead of Lynch Road in Detroit where corporate could keep an eye on it?
Have other Super Bees with similar VINs and SPDs ever surfaced?
Why does this tag code differently than other known Super Bees?
Is the tag coding consistent with other Coronet cars built at the LA plant about the same time?
LA cars are notorious for not having Broadcast sheets. I presume this car does not have one either.
Is there a window sticker? IBM card or any other factory document that mates the VIN with the SO?
One thing about the '68 and earlier cars is that they are easier to fake because there is no way to directly tie the body to the VIN tag.
Known bad VIN and fender tag cars exist.
Can you check the date codes on the back of the Rallye Dash? You should find date codes on some of the gauges and the total assembly.
Assuming it's original, can you check the date code on the radio?
Radiator?
Wiper motor?
Since the hood is a '69 hood, I presume the date code on the hood latch is from '69.
Assuming the rear end has not been switched, have you checked to see which rear end carrier the car has?
The more of these components that do not match the SPD, the more the curiosity level should go up.
What do you actually know about the history of the car?
Who put the hood and '69 interior in the car? When?
How fresh is this restoration?
What do you know about the chain of ownership?
Which owners can you call to verify the history of the car?