While the first GT-350s were rated at 306 HP, 35 HP more than the 289 K code engines they were based off, you are correct, due to emissions regulations the 1968 Shelby GT-350s came with the same old ordinary 250 HP, 302 CID, 4BBL, hydraulic lifter engine that regular old Mustangs got. Later in the year the GT-350s did get aluminum intake mainfolds (after emissions approval).
It is also questionable that the 1967 GT-350s really had as much HP as the 1965 & 1966 GT-350s as the 1967s did not have the long tube headers that the 65s & 66s did.
In any case to me a real new GT-350 would need to have 35 more HP than a regular Mustang GT.