In 1969, the 390 was actually a 390IP (Improved Performance). Not a 'GT' motor. They made some changes to the cam and changed the carb. The specs for that motor actually prove it was a reduction in performance in that it went from 325hp in 68 to 320 hp in 1969. They did this to boast the new 428 engine option available in 1969.
Docs I have on Ford Engines note S "390GT" was 66-68 only. 66 in Comet and Fairlane, added to Cougar and Mustang in 67, dropped from the Comet in 68 and added to the Montego. As noted the 390IP was the S code for 69, so not all S codes are 390GT's.
I've also seen 67's referred to as "390 Thunderbird Specials", not 390GTs'..???
Not quite sure what you mean by a "GT" motor. The s-code indicades a 390 cdi, 4 barrel factory engine. They can be found in non "GT" cars, like mine. (Go figure, I have an S-code GT/CS that came without the GT option!)
I don't recall any of the FE engines being called a "GT"
As noted the "390GT" confuses a lot of people into saying they have a "GT". Looked over a couple Ford brochures for 67 and 68, neither mentions the "390GT" only the "Thunderbird Special" for the S code. In 68 the X code 2 bbl is noted as the "Thunderbird V-8".
In addition to the 4bbl carb a 390GT differed from a "standard" 390 with a different cam, higher compression (10.5:1 vs. 9.5:1) and "special" ignition components (not specified in my references). On the visual side, 67 got a unique no snorkel dual screen air cleaner w/chrome lid, 68 got the chrome dress kit (valve covers, oil filler cap air cleaner lid), not sure about 69....
Would be interested if anyone has any good references/links on this issue as I am trying to gather info on these engines and details on the year-to-year differences.