Does anyone know how many 1968 Barracuda 340 formula s fastbacks were produced?

Did all of the 1968 formula S cars have the rocker trim originally?
No. There were two types, and they were extra cost as stand alone options or part of a package. The "Custom Sill Moldings" (gills and spears) were included in a Spring Special package.

*Edit-
Here's an advertisement for a special package in which they were included on the notchback, but not the convertible or fastback.
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