You got a lot of questions there!
Is a 38 3 speed shorter than a 50s 4 speed? I would say yes off the top of my head, but I would have to measure to be sure. By 50s 4 speed I believe you are referring to the sm420 with the granny low. I am cornfused as to weather or not is is an open driveline or a torque tube setup.
In my 1940 GMC I will use the original bellhousing so I don't have to "rube" the pedals. I made an adapter plate so I could put a NV4500 5 speed transmission. I will have to use an open drive rear end.
Suggestions... A T5 5 speed is pretty eazy to adapt in our old trucks... there is a tech tip on installing a T5 in an art decco truck. Your prewar truck is virtually identicle to the art deco trucks. If you already figured out how to mount your pedals on the later 50s bellhousing, the T5 will nearly bolt right up without an adapter plate. But you will have to extend the splines, and possibly have to cut a little bit off the snout to make the clutch work.
Find a suitable rear axle... a lot of people use camaro rear ends, and then match the front with disc brakes. If you still want to keep the 6 lug bolt pattern, you could probably use a 55-59 chevy or gmc 1/2 ton rear. I know they sell 5 lug front disc brake conversions for your truck. 6 lug is doable, but you have to do a little more work. You would have to locate a 41-54 1/2 ton front axle and swap that into your 38, and then you could get a 6 lug kit for that axle.
You have a lot more options if you go with an open driveline over a torque tube.