Since you have a 4 speed you may already have some parts that you can use with the later Ford toploader 3 speed. Some of the HD transmissions had a special adapter. There was the regular bell housing engine adapter, then there was a round front, flat back adapter between the bell housing and transmission. This may have been for the HD 4 speed and lager transmissions. Through that transmission adapter is the throw out bearing and clutch rod. The regular LD transmissions just used the one adapter instead of two, the throw out and clutch rod went directly into the front of the transmission housing.
This transmission adapter is also produced new. Basically that adapter allows you to bolt a later model transmission to the flathead and you can still use the original clutch linkage. Jeep used the Ford 303 design in mid 70s Jeep CJ 5s and 7s.
So with the clutch adapter mentioned, original or repro, you can bolt the 60s Toploader 3 speed to the flathead. The 70s Jeep CJ transmission shift tower and forks will fit on top of the toplader, as they are the same transmission. The shift tower will go through the same hole as the original F-1 3 or 4 speed. The only modifications will be removing the side shift forks out of the Toploader, and tweaking the transmission mount. Some say you have to slightly grind the input shaft at the pilot bearing for the correct length. The 64 transmission used the same heavy spline as the F-1 so for that one no driveshaft modification is necessary but the 64 has no rear mount so one will have to be fabricated.