The best info I can find is the screw is Ford p/n 56301-S4, 1/4-20X1/2HH,REC,FLNG9/16,3/8HEX,GR5,UBS. The screw is listed in the "1970 Mustang Interior Assembly Manual" (AM0032 pg 37) - there is no published 1969 Mustang Interior Manual, and in the 1975 "Ford Car Parts" (aka MPC) interior trim illustrations section (section F, pg 9). This is an assumption based on the designs of the 1969 and 1970 Mustangs are very similar.
(Note: AMK lists the screw for sale as being 5/8 in long overall, but shows the screw threads as 1/2 inch long (the lead point is not measured) in the "AMK Guide to Ford Fasteners" pg 143.)
To verify what was used in 1969, someone is going to have to remove a screw from a car and measure (including a picture) the screw.
Jim