First, again: it's a great car.
Racing screen: OK, we wanted whoever won it to be able to drive it on the street, so it's got a windshield
Yes you are right.
Gauges: I've never seen a picture of the original's dash that was close up enough to see the gauges, so I don't know. The layout is same as the original.
See pic:
Fenders: Original had slabside front fenders, raffle car has slabside front fenders...what's different? Front fender extentions, where the decals were located

Rear fenders are the same as the original when it was it belonged to Coventry Motors. Shelby apparently flared them out some more later. No, see picture:
No jacks: Original did not have front quickjacks when raced by Allen Grant. And no rear jacks, see pic.

They were added after the car went to Shelby.
Meatballs & Numbers: From all the pics I've seen, they're the same. They have to be bigger, see pic.
Mirrors, latches, and pop rivets: Yeah, those are different.
Black grille: ??? Neither the original or the replica have a grille, When yellow it had one, see pic
Wheels: Nobody makes real knock-off kidney bean wheels in 15". I don't know why...
Doors: Both the original and the replica DO NOT have cut-back doors, despite the text on the Shelby museum page. Yes the car has, see pic
Switches: Original had additional panel with 7 switches, replica has additional panel with 7 switches. They're even labeled with an old-school Dymo labels. I can only see 6 on the replica
Brakes scoops: Looking at the pictures above, you're right.
Gas cap: Splash guard was added after going back to Shelby. Don’t mean a splash guard, see pic
Raffle car doesn't have the flat-head Cobra badges like the original - anyone know where we can get some??? When yellow it had the later emblem, when back to Shelby it was the flat-head Cobra, don’t know the reason, see pic
