The CJ manifolds flow much better than the GT manifolds. Both use the same bolt pattern with the vertical only used on the rear driver side. And there were some 14 bolt CJ "N" heads that were used and found on the 68 Cougar GTE's with the 428CJ engines. As KD said the rest were all 16 bolt pattern. What is the application you want to use the GT mani's on?
The CJ repops are close to $500. And the originals are a bit more pricey due to the CJ/SCJ restoration costs going thru the roof. But you can find some deals on them every now and then. A nice set of original GT mani's are in the $300 range. Besides being used on the S and X code Stangs and Cougars they were alos stock on the 68 427 GTE Cougars. Personally I'd just use the GT's for now as they fit well without issue and you have them. You can always shop for the CJ's or even a nice header down the road if you want more.
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