I discovered the uniqueness of the F-100 overdrive last year while helping a friend try to put overdrive into his 53 pickup. I thought we could take a 53 car overdrive and his 53 truck transmission, mix and match the parts, and have a nice result. We got close, but found out to our sorrow that the truck overdrive input shaft is unique to the trucks, and none are out there to be had.
If strict originality isn't a concern I suspect any 1953 through 1964 F-100 overdrive transmission would work. The later years used the Borg-Warner T-86 transmission instead of the Ford unit for the three speed portion, but I think the important dimensions are the same. I have seen a 1963 F-100 overdrive transmission and the input shaft, bolt pattern, and transmission length looked the same to me. The driveshaft yoke would probably need to be swapped for a fine spline part if a later transmission is used. This information probably doesn't help much since these are also rare transmissions. Also, a disclaimer, I have not personally swapped a later F-100 transmission into an earlier F-100.
Here is a picture of the greasy 1963 F-100 transmission for reference.
