All 390 4V/S codes installed in Mustangs came with Thermactor systems. - at least those originally sold in the US.
X codes (390 2V's) did not.
In 68 Ford changed (because it was required to) having the same requirements for emissions systems throughout the country for Mustangs and all their engine types. For other engines (no 390 and 248's) the difference was sometimes the type or transmission ordered but that was not the case for 390's