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Don't know if all 409 cars were this way, but I recall the high performance cars had two upper control arms and two lowers on the rear end instead of just having two lowers and only one upper.
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John, Chevy never built a 61-64 409 car with two upper rear control arms, not even the Z-11s. IT was common for people to add one though. It probably helped a little bit, but the left (added) one was actually mounted on the edge of the pumpkin due to the offset of the pumpkin. There was still nothing to prevent the left axle tube from twisting. (tell me how I know that

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As far as determining whether a car was originally a 409, if the car is restored with all new & repro stuff, it's practically impossible. A reliable paperwork trail, owner history and pre-resto photos are the main proofs.
Verne