The moulding clips for which you are looking, are shown in illustration "C" in the attached copy from the 1960-68 Ford Master Parts Catalog. The second picture is from the 1967 Body Assembly Manual and shows the clip going into the square hole as you mentioned. Note that there is no solid "star" by the part in question. This is usually a good sign as the solid star signifies that the part is "Not Serviced". Also, in the Text Section (copy attached), there is no notation that the part is "Not Serviced" as sometimes would appear. Yet, in looking at the Ford November 1966 and May 1967 Ford List Price Books, this part does not appear. This tells me that this clip was not available separately.
However, all is not lost. The Moulding itself, Part Number C7ZZ-6342512-A, was shown as "Includes Attaching Parts". This part was available in 1967 for a "whole" $2.35, including the attaching parts ! So, you could look for the entire moulding, assuming that someone hasn't robbed the attaching parts out of the package. Otherwise, you will have to do as Jeff noted and find a donor car with the clips on it, or luck out and find a bag of the attaching parts that someone only needed the moulding, and had the forethought to save the attaching parts. Unfortunately, this part was used only on 1967 Mustangs ; no other Models, including the 1968 Mustang Fastbacks. Also unfortunately, I know of no faithful reproductions currently being made of this part.
Hope this helps.
Bob