I caqnnot tell if you have the gearcase off. I will assume you don't. Usually those mechanical shift motors have a hatch on the midsection, and another hatch under that in the exhaust passage. Under the second hatch is the shift rod connection. The bolts must be removed to separate the shift rods. Loosening them is not enough.
A lot of those motors have a driveshaft that will pull out of the gearcase, with no effort, once the waterpump is removed.
The 5" extension should unbolt from the midsection.
If you want to convert from long to short shaft, you usually need a new short driveshaft, and a short shift rod connection. The water tubes can have extensions on them. However, I do not have experience with all motors of that age, so things could be a bit different.