Based on a few sources I have come across, out of the 81,722 GTOs built for the 67 model year, 39,128 were built with manual transmissions. Now that numbers is an overall total of all non-automatics, which includes both 3 spd and 4 spd manual trans.
So to answer your original question, yes manual trans was offered, and yes, automatics were more popular, 42,594 vs. 39,128. Pretty close to 50/50.
However, on the classic car market, the manuals, especially the 4 speeds will be the most sought after. Maybe they are just not as many is the sales stream right now because those who already have them don't want to part with them.
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