The production reports don't break it down to body style, only by series.
3000 series = Special
4000 series = Skylark
There were 5845 Skylarks built with the 4 speed option, or about 4.5% of the 4000 series Skylarks. That includes 2 doors, 4 doors and wagons, and GS's.
For GS convertibles, about 28% came with 4 speeds, 598 cars.
So there's a range from 4.5% (all Skylarks) to 28% (GS) for 4 speed cars, or 622 to 3874.
I'd guess 10-15% 4speeds would be more reasonable for the 13,837 Skylark convertibles, or 1,383 to 2,075 cars.