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There is an adapter plate available to bolt an AOD to the flathead, saw it on Wheeler Dealers 2-3 years ago... I'm sure there are some available for the C4 and 5 speed as well. Speedway has several to choose from, depending on how much you want to spend.
I went Tremec T5 in mine. I opted for a Ford T5 because it has heavier shafts and I like the gear rails better. I had to but an adapter plate from DL, a clutch for mustang, a bushing for the inside of the release bearing to fit the transmission properly. I also went with an S-10 tail shaft housing to move the shifter forward and a speedo gear relocate kit to use a manual speedo. I haven't driven it yet as I am still building it but I am looking forward to it :-)
2nd the tremec, I went with the tko500 complete kit from speedway. Also got the kit to move the shifter to the middle location of the tko500. 51 f3 with original 4.86 gears but cruises 60 easily.
Keep in mind the '53 is different from the earlier trucks. It has a single center engine mount in the front. All of the lateral support is through the mid-engine mounts on the bellhousing. (See the picture below)
Unless they have something new that I have not seen, the automatic kits offered by Speedway will not work on the '53 Ford truck. (I was wrong once before, it could happen again.)
It is possible to use an engine mid-mount plate for automatics, or to weld brackets to a steel bellhousing for the mid-engine mounts for a manual, but changing to a non-offered transmission in a '53 F-100 will take some careful planning and execution.