The 1969 Cougar was available with a 390-4V IP engine. The last year for the 390 GT engine was 1968. Look in the 1969 shop manual.
The 390IP engine in your 1969 Cougar had a milder cam and the Autolite 4V carb was used to meet emissions standards. The 1968 390GT used the Holley 600 CFM 4V and needed Thermactor smog pump to meet the same emission levels. Ford saved big bucks by not having to install the smog plumbing and horsepower was only down a little.
Here's a link to what CCOA says about the years the GT package was offered. They claim it was an option in 1972 also, I have to check on that. As you can see it also is silent on 1969 because there was no GT option for the 1969 Cougar.
Now when you read the VIN and you come across the "S" code which I understand is a 390 is it the same in 67-68 as in S=390 so whats a give away to tell the differance? I couldnt pull the page up.I learned something today.I knew the truck engine 390 was different.I thought that was all 390 and the 390gt.