V12

Are you asking about the Zephyr or the K engine?

The gears are interchangeable, I believe, between the Zephyr and the '39 and later Fords but, the gear ratio's are different and there is two different gear ratio sets for the Zephyr.

The Zephyr tail shaft housing is longer, at least for the OD trans.
 
They also had different cases. As was mentioned, the tail shaft was longer for the OD unit and it had a different mount set up for the frame but they were still closed drive set ups. The ones prior to the change to side shift had a different shifter set up and not all were overdrive type units but the input, cluster, and 2nd gears generally were interchangeable with Ford units. here is a link to the different cases.
http://www.vanpeltsales.com/FH_web/flathead_transID_3speed-options.htm
 
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