Since the Atomic 4 descended from a World War II lifeboat engine, it featured some very old technology.
One feature was the transmission design. It requires so much force to shift into reverse that it must have a larger control cable than more modern engines.
This stainless steel clevis, #Z3094 is perfect for the pedestal end of the cable, but not the thick control arm on the transmission
An unusually large shift lever
In fact, is so much force is required to shift that the shift lever mounted to the transmission is larger that anything else on the market today. It is very wide (thick) with holes drilled for a 3/8" clevis pin. Unfortunately, if your old clevis and clevis pin are no longer usable, there is no replacement available that is wide enough to fit over this thick lever without modification. The stainless steel version used inside of the pedestal is not wide enough.
This zinc plated steel clevis was available
at the time of this writing (1/2017)
One possible source
We contacted Moyer Marine (https://www.moyermarine.com) who are the Atomic 4 experts. They also don't have a ready-made solution. They report that their reproduction Atomic 4 shift levers are arriving at 0.51” to 0.55” wide. As you can see, that is too thick for even the steel clevis, but it is close.
Midwest Control Products has a steel clevis that you might modify: try here. It reportedly has an inside width of .438".
This transmission lever and the clevis from Midwest Control have been modified to fit
Some modification will be required
The only option we are aware of is to file the clevis a bit wider and grind the lever a bit narrower to achieve a good fit. Since the clevis must rotate on the pin when you shift the transmission, be sure there is enough space to allow free motion of the lever between the ears of the clevis.