[Flathead Fever]

On a synchronized transmission you usually shift the gears into the neutral position by moving the synchronizers. Then put the shifter (forks) into the neutral position and the forks should just drop into place.

In your trans there are no synchronizers so you need to slide the gears into their neutral positions as shown in this drawing. With the shifter also in neutral it should drop down flush with the trans case.

Once you have it figured out. With the top off its also a good time to add your gear oil. Its a lot easier to pour it in that big opening up to the filler plug level.